After falling to a 2-0 deficit after just 12 minutes at the Allianz Arena, few would have predicted anything other than a defeat to the German giants.
However a David Silva effort in the 28th minute sparked a fine comeback, which was eventually capped with an Aleksandar Kolarov penalty midway through the second-half.
With qualification for the knockout phase already secured prior to kick-off, Pellegrini elected to rest a number of key players, including top scorer Sergio Aguero and influential midfielder Yaya Toure.
After the game the Chilean said that his decision was justified, and that his side proved they are equal to the very best teams in the competition.
“It was a very important game. First of all because we wanted revenge for what we did in Manchester – we played very badly that day,” Pellegrini told Sky Sports.
“There is not that difference between Bayern and our team.
“So, today, winning here and scoring three goals without Kompany, Aguero, Yaya Toure, Nasri, I think that shows we have a very good squad, so it is an important victory.”
Thomas Muller and Mario Gotze opened the scoring for Bayern, before Silva, James Milner and Kolarov netted for the travelling side.