The Champions League holders surrendered a two-goal lead to lose 3-2 at the Allianz Arena on Tuesday and their coach believes the result will serve as an important wakeup call.
Thomas Muller and Mario Gotze had put the holders in control after just 12 minutes, but goals from David Silva, James Milner and an Aleksandar Kolarov penalty secured a memorable comeback for last season's Premier League runners-up.
"I think it is something we have to know - that we can lose," Guardiola told reporters after the match. "Opponents have good players and coaches too. It is always difficult. But we started very well and for the first 30 minutes we were very good. Later we had to use the ball better and use our counterattacks. Manchester City are a good team and you have to have more than just possession.
"Congratulations to Manchester City on this great victory. Sometimes you need to lose a game. In the Bundesliga we have won everything, in Manchester we won 3-1, but now we lost and have to cope with that. But we're already looking ahead to next week in Marrakech [for the Club World Cup]."
Bayern finished on top of the group despite the defeat to Manuel Pellegrini's men and Guardiola believes his side should be congratulated on its performances during the group stage.
"In the first half we did not make many mistakes, but during the first 10 minutes of the second half we did not play very well. In general we are satisfied," he said. "We met a great team in the group phase; Manchester City played quite well tonight.
"I congratulate the players on their success and I hope we understand now how difficult it is to play in Europe. We did not always have the right player in the right place on the pitch. We have to work on this – that is the lesson we learned today."