Hernandez opened the scoring for Bayern in Tuesday's 2-0 Champions League victory and played a full part at the Allianz Arena.
However, the 2018 World Cup winner suffered an injury during the match and is now facing a spell on the sidelines.
No timeline has been given by Bayern for Hernandez's recovery, but widespread reports suggest he is facing four to six weeks out of action.
That will see Hernandez miss France's upcoming Nations League games against Austria and Denmark – Les Blues' final fixtures ahead of their World Cup title defence in nine weeks' time.
Didier Deschamps has been hit by a number of injury issues ahead of naming his squad on Thursday, with the likes of Paul Pogba and Karim Benzema also nursing fitness problems.
In more positive news for France and Bayern, Benjamin Pavard has confirmed the knock that forced him off early on against Barcelona is nothing serious.
Hernandez, who can play at both left-back and centre-back, has started eight of Bayern's 10 matches this season.
UEFA has suspended the Champions League and Europa League indefinitely during the coronavirus pandemic.
President Aleksander Ceferin said last week that he would consider allowing those European competitions to resume behind closed doors if necessary, likely in July and August, but he accepted they might have to be cancelled if they were unable to resume matches by September.
With Europe's top leagues also facing the prospect of having to be completed in July or later, Hernandez does not think it will be practical to stage the final rounds of the Champions League at the same time.
"It's going to be hard to cram all this in as well as a possible end to the league," he told L'Equipe.
"The Champions League concerns all the countries affected by coronavirus. It will be difficult to get everyone out of lockdown, to be in similar condition but also just to meet up, to travel to Italy, Spain, England or France.
"You have to be realistic. I think it will be impossible to finish in the Champions League in these times, especially if we favour ending the domestic leagues."
Clubs in the Bundesliga have been allowed to resume first-team training, albeit with strict restrictions in place on the number of players assembled at any one time.
Bayern kept players in separate small groups to adhere to social distancing guidelines after beginning training at Sabener Strasse from last Monday.
"The conditions are very strict. We are in small groups of four. We do not meet the others," Hernandez explained.
"We train at different times to avoid contact. The changing rooms are also arranged differently. We don't occupy the same pitches.
"But as soon as it's over, we'll quickly go and shower and eat at home. This is another way to get the machine up and running again."
The award – given to the best under-21 player in the world – went to a Barcelona midfielder for the second year in a row, as Gavi replicated Pedri's 2021 success.
Bundesliga duo Musiala and Bellingham were both in contention for the prize, finishing third and fourth in the voting respectively, with Real Madrid's Eduardo Camavinga coming second.
Asked about Musiala's failure to land the award ahead of Bayern's trip to Augsburg in the DFB-Pokal, Nagelsmann said: "You wear club glasses.
"In my eyes, both Jamal Musiala and Jude Bellingham have had better seasons than the winner. Gavi is an outstanding player, and I'm happy for him too."
No Bayern player has bettered Musiala's return of five league goals this season (level with Sadio Mane and Leroy Sane).
Meanwhile, Borussia Dortmund midfielder Bellingham last week followed Kylian Mbappe and Erling Haaland as just the third teenager to score in four consecutive Champions League appearances.
Attention for Bayern now turns to the DFB-Pokal, which they last won in 2020.
Their bid to go beyond the second round this season could be hamstrung by the absence of Manuel Neuer, but Nagelsmann is not prepared to take any risks with his shoulder injury.
"It's not a conscious pause. Anything in the shoulder area is unfavourable for a goalkeeper," the coach explained. "If you have a sharp pain, you can't react.
"He has pain when moving and is therefore restricted. As a goalkeeper, it's impossible to get 100 per cent performance then, so it doesn't make sense [to play Neuer]. It would be easier with an outfield player.
"We do everything in the necessary care for the players. We try everything to prevent this and consult all possible values. The rhythm is what it is. It's annoying when players are out and injured."
Nagelsmann also offered an update on the condition of Lucas Hernandez, who he hopes will recover from a muscle tear before the World Cup begins next month.
"It's looking better. We're making a bit more of him," Nagelsmann said of the defender. "We have to be patient. I can't say how long it will take.
"It hasn't been looking too good lately. He's making progress, but it's a tough injury. I hope he can play at the World Cup."
