Aguero's goal in the fourth minute of stoppage time snatched the trophy from holder Manchester United on goal difference. The 2010 champions had been top when its game at Sunderland ended in a 1-0 win.
Pablo Zabaleta had put City on course for the title with a 39th minute-goal, but Djibril Cisse levelled for QPR three minutes into the second half after being gifted possession by Joleon Lescott.
City had a man advantage after QPR captain Joey Barton was sent off in the 55th, but Jamie Mackie managed to head the visitors in front.
City's expensively assembled squad had been facing its first loss at home since December 2010, but substitute Edin Dzeko sparked the recovery by heading in a corner in the second minute of stoppage time.
There was still time for one final moment of drama in an unpredictable season when Aguero drove home the winner.
As the final whistle blew, thousands of City fans poured onto the pitch and blue smoke wafted around the stadium.
City's title comes after more than a $1 billion of investment by Abu Dhabi's Sheikh Mansour, who took over the financially stricken club from ousted Thai Prime Minister Thaksin Shinawatra in September 2008.