Despite leading through Aguero's 22nd-minute penalty and playing against 10-men thereafter due to Mehdi Benatia's sending off, City looked set for another night of disappointment in UEFA Champions League Group E after Xabi Alonso and Robert Lewandowski gave Bayern a 2-1 half-time lead.
That scoreline remained until the 85th minute, when Aguero capitalised on an Alonso error, and the Argentina marksman completed a remarkable turnaround by securing a 3-2 triumph in stoppage time with his 17th goal in 18 games this season.
Despite taking five games to secure a first Champions League win of the campaign, victory at Roma in their final group game will see City through to the knockout stages, providing CSKA Moscow do not follow in their footsteps by beating Bayern.
And Pellegrini was quick to pay the highest praise to his match-winner.
He told Sky Sports: "I always say that Sergio is one of the five best players in the world so I believe every time he plays he must play in the way he did today - with this intensity and concentration.
"I repeat, he is one of the best players in the world."
Pellegrini also credited his team's collective effort, as they probed for an opening throughout a second half where they struggled for fluency.
"I'm very proud because I think it was a very difficult game for us after Bayern scored those two goals," he added.
"We couldn't find the space to create real danger by their goal so I think the way the team worked for the whole 95 minutes and the way we trusted in what we do was one of the key factors."
Frank Lampard was an assured presence throughout in a City midfield missing Yaya Toure and Fernandinho through suspension, along with knee-injury victim David Silva.
"It was a special night in the end - we kept believing," the former England international told Sky Sports, before turning his attentions towards Aguero.
"Especially with them having 10 men, there were spaces at the back, and thank God we've got that man up front.
"He's something incredible. When he runs through you expect him to score.
"He's at the top of his game and one of the top strikers in the world."
