The Parisiens needed a stunner from Achraf Hakimi to salvage a point at the Parc des Princes after Noa Lang had given the Eredivisie outfit a 34th-minute lead.
Luis Enrique's side have struggled in this year's competition, with Hakimi's leveller only their second goal in the Champions League this term, despite netting 25 goals in Ligue 1 this campaign.
PSG dominated for large parts on Tuesday, registering 26 shots, the most against PSV in a Champions League match since November 2018 (30 from Tottenham).
Luis Enrique's side have also now had 25 or more shots in each of their last three Champions League home games (also 30 against Borussia Dortmund and 26 against Girona).
"Efficiency was our main problem because we had a lot of chances," Marquinhos said.
"We had so many opportunities in the beginning but did not convert, while they were more clinical, opened the scoring, and it changed the scenario of the match."
But for all of PSG's attempts, only eight were on target, with the Parisiens underperforming their expected goals (xG) total by 1.57.
Ousmane Dembele struck the woodwork in the 18th minute, while Bradley Barcola and Lee Kang-In threatened, but they rarely threatened visiting goalkeeper Walter Benitez.
"We are among the teams who create the most chances, the team are playing the way I want them to," said Luis Enrique.
"If you look at the statistics, we've been scoring a lot of goals," added Marquinhos, referring to their 25 in the opening eight Ligue 1 games this season.
PSG currently sit 17th in the new Champions League table ahead of Wednesday's fixtures, with games against Atletico Madrid and Bayern Munich to come.
"Our style of play has changed," Marquinhos said. "We need to be more calm in front of goal.
"These are things we need to work at in training and in our heads."
The 3-0 loss, in which Wissam Ben Yedder scored a double either side of Kevin Volland's goal, is the heaviest defeat PSG have suffered in Ligue 1 since a 5-1 loss at Lille in April 2019.
PSG have now lost three of their last five games in Ligue 1, as many as they did from their previous 36 matches (27 wins and six draws).
It also represented PSG's heaviest loss to Monaco since September 1999, when the principality club defeated them by the same scoreline in Paris, and Marquinhos did not hold back in his criticism of the display.
"It's hard to digest. It's our worst game of the year," he told reporters.
"We came here to have fun and win a game. We are in a difficult moment.
"You can't just throw it all away. We all have to work together to get out of this moment."
Marquinhos stopped short of suggesting that PSG's recent Champions League elimination at Real Madrid has led the team to drop off, but claimed they could still lose their 13-point Ligue 1 lead without major improvements.
"It is not a relaxation," he added. "There were a lot of expectations [against Real Madrid]. It's a defeat that hurts us.
"Now we have goals to look for. We have to do our best, with the right mentality.
"If we continue to perform like that, it is sure that the title is in danger. The alert is there. We will have to come back [from the international break] with a good state of mind."
PSG boss Pochettino has now lost eight of his first 50 league games in the Parisian dugout, the same amount that his predecessor Thomas Tuchel suffered in his first half-century of matches.
Pochettino repeated Marquinhos's criticism of the performance after the match, calling his team's display "unacceptable".
"It is inadmissible to start this way," Pochettino said of PSG's dire first-half showing. "Afterwards, there is sporting shame.
"Now we have to move on, get over the frustration of the Champions League and think about giving our best, and have a competitive spirit.
"This is unacceptable. This first half is unacceptable. We didn't have a fighting spirit, the way we played is not acceptable.
"This cannot happen, we can have [bad] performances, but this type of attitude is not possible. It's unacceptable to start the match this way. Respect for the club, [and for] our supporters, is essential."
Bayern beat PSG 1-0 in last season's final, Paris-born Kingsley Coman getting the only goal in Lisbon.
Since then Pochettino has succeeded Thomas Tuchel as head coach of the capital club and, as such, he views Wednesday's quarter-final first-leg encounter at the Allianz Arena with a certain level of detachment.
"No, it's not a benchmark match for us," Pochettino told a pre-match news conference. "We weren't there with my staff, we were just spectators. In addition, it's over two matches that it's going to be played, the context is different.
"Sporting revenge still exists, but for us it's more of a challenge to beat such a strong team, maybe the best in the world."
Even their most ardent supporters would struggle to apply such a label to PSG at present after a 1-0 weekend loss to leaders Lille left them facing an uphill battle to retain their Ligue 1 title.
Neymar, sent off during that frustrating Parc des Princes encounter, is available to line up alongside Kylian Mbappe once more and the star forwards will hope to exploit Bayern's high line to a greater extent than they managed in last August's showpiece.
PSG's capacity to create for Neymar and Mbappe will be compromised by Marco Verratti's absence after the Italy midfielder returned a second postiive COVID-19 test this season.
"Each team has its characteristics, Bayern are a well-organised team with a high defensive line," Pochettino said.
"Their attacking players can throw opponents off balance and make a difference. It's up to us to make sure we don't lose the ball in dangerous areas."
Bayern's forward line will lack their injured talisman Robert Lewandowski, while Serge Gnabry is also set to miss the tie after testing positive for coronavirus.
There will still be plenty of problems to nullify for Marquinhos and his defensive colleagues, although the PSG captain aligned himself with Pochettino despite having experienced the heartbreak in Lisbon first hand.
"There is no revenge compared to last season, it is another context, each game has its story," he said.
"If some people want to use that to motivate them, why not?
"The finals are played on small details, you have to take the few chances you have. Tomorrow it will be the same.
"They too know that they will have to take their chances. Everyone is aware that it will be played on details."
The five-time world champions were beaten 1-0 in Asuncion, with Diego Gomez's 20th-minute strike condemning them to a fourth defeat in five qualifying games.
Dorival Junior's side occupy fifth place in the CONMEBOL section - in which the top six nations automatically qualify for the 2026 World Cup, with the team finishing seventh entering the Inter-confederation play-offs.
Already eight points adrift of leaders Argentina, Brazil are now just one ahead of eighth-place Bolivia, and Vinicius knows he and his team-mates must do better.
"We apologise to the fans, who are always on our side," the Real Madrid forward told Sportv. "But this is a difficult time, we just want to improve.
"I know my potential, I know what I can do for the national team. Of course, it's been a very difficult process, because when you don't have confidence, you don't get goals, you don't get assists and good performances.
"We know the situation we're in, we want to get Brazil out of this situation at any cost, we all have to go home now and start thinking about what we can do to get back to playing well.
"We cannot come here, lose these points and play the way we did. It is a difficult time, we must take on board all the criticism and return as quickly as possible to put Brazil on top."
Meanwhile, Marquinhos believes Brazil are going through a transitional period, and that they are not brimming with belief as a result.
"The coach is still figuring out the best way for us to play and that's reflected in the result," the defender told Brazilian TV Globo. "There are a lot of new players, we are lacking confidence.
"Qualifying isn't easy, it's a difficult time, and we have to know how to manage it. It's a time of transition, we're not feeling confident. We're going to work hard, getting results on the pitch is the best answer."
