Right-back Munoz acrobatically converted Luis Diaz’s cross in the 61st minute to earn his side a morale-boosting result moving towards this summer’s Copa America in the United States.
Three-time European champions Spain enjoyed plenty of possession at the London Stadium but lacked a cutting edge as their eight-match winning run ended.
Former Real Madrid man James Rodriguez played an instrumental role in his country’s success, which stretched their unbeaten run to 20 games, after coming off the bench following a forgettable first half.
Spain will look to bounce back on Tuesday night when they host Brazil at the Santiago Bernabeu in Madrid.
The Spanish – unfamiliar in yellow shirts against a nation renowned for wearing them – opted to leave influential Manchester City midfielder Rodri on the bench for the evening, while Liverpool’s Diaz captained Colombia.
Luis de la Fuente’s side started in the ascendancy but without seriously threatening in a tight opening period of few chances.
Athletic Bilbao defender Daniel Vivian nodded narrowly over on his international debut following a fine cross from Alex Grimaldo, who earlier fired straight at opposition goalkeeper Camilo Vargas.
Colombia, backed by a sizeable support at the home of West Ham, were aggressively pressed by a team monopolising possession.
Mateo Cassierra forced a save out of Arsenal goalkeeper David Raya following a well-worked free-kick routine but the South Americans were restricted to little as they largely sought opportunities to counter.
Colombia manager Nestor Lorenzo turned to James in search of a much-needed spark for the second period, while Spain keeper Raya was replaced by debutant Alex Remiro of Real Sociedad.
Lorenzo’s men improved significantly after the restart, albeit Vargas had to be alert to deny Gerard Moreno a 49th-minute opener.
Minutes after skying well over when well placed, ex-Everton player James played a key role in what proved to be the winner.
His fine pass released Diaz down the left and, after twisting and turning Vivian, the skipper delivered an inviting centre which bounced before Munoz, winning his 24th cap, dispatched the ball high into Remiro’s net with an eye-catching scissor kick.
The thumping finish sparked wild scenes of celebration among the healthy Colombian contingent in a crowd of more than 43,000.
Spain introduced striker Alvaro Morata as part of a triple change.
But they could not find a leveller as they slipped to a first defeat since a shock 2-0 European Championship qualifying loss to Scotland last March.
Miscommunication between VAR Darren England and referee Simon Hooper led to a Luis Diaz goal for Liverpool at Tottenham being wrongly disallowed last month, leading to further calls for such conversations to be played out in real time.
The incident caused huge controversy, with Reds manager Jurgen Klopp even calling for the match to be replayed.
Broadcasting the conversations between on-field officials and VARs live is currently prohibited under football’s laws.
Bullingham, who is a director at the International Football Association Board (IFAB) which has the power to change the game’s laws, said the organisation had discussed the subject but added: “Generally there is a split in the room over that, and quite often it is between the marketing and commercial people and the referees.
“Our point of view, from the marketing and commercial perspective, would normally be that transparency is a really good thing, and we want fans to have the maximum experience.”
Bullingham said an ongoing FIFA trial where referees announce and explain the outcome of an on-field review is a “step in the right direction” but added: “My personal point of view is I do think (live audio) will continue to be a question over time, because the greater transparency shows how difficult the referee’s job is, and it has worked in other sport.
“There is an understandable nervousness from others that the referee’s job is hard enough as it is. In a tournament you have referees with multiple languages, so it is not as straightforward as some might suggest.
“So I think we are taking a step in the right direction with announcing the decision and explaining why it has been reached. Let’s see if that leads to further progression.”
Bullingham’s Irish FA counterpart and fellow IFAB director Patrick Nelson spoke more cautiously on the VAR decision-making process, adding: “We just need to see more evidence on this at the moment.
“It’s interesting when we look at recent examples but we still need to remember that VAR as an entire concept is relatively in its infancy compared to the game of football and compared to IFAB. There is still more that we can learn.”
The PA news agency understands the IFAB is set to open up the trial of in-stadium announcements by referees beyond FIFA events to other interested competitions.
The IFAB may also look again at the wording of Principle 10 in the VAR protocol, which currently prevents VARs from revisiting a decision once play has restarted and meant the officials could not call play back after the Diaz error.
It could be updated to allow a decision to be revisited where a clear mistake has occurred, and where no significant action has taken place since play restarted.
Bullingham also said he was aware IFAB had been asked to consider widening the scope of VAR to rule on decisions such as corner kick and free-kick awards.
“I think we would be really reluctant to have a game that was stopped a lot more than it currently is, but that will be a proper discussion,” he added.
VAR interventions are currently limited to goals, penalties, straight red cards and mistaken identity.
