Time and again QPR's defence held them off, but the equalizer finally arrived in the first minute of stoppage time when Edin Dzeko headed home a corner kick to give City a lifeline.
With Manchester United have claimed a 1-0 win at Sunderland, City still needed another goal to win the title, and the dramatic moment arrived just before the final whistle when Mario Balotelli's return pass allowed Aguero to fire home the title-winning shot from 10 yards.
The result could have been a disaster for QPR, but the club was spared the agony of being relegated as Bolton was held to a 2-2 draw at Stoke City.
Manchester United 1, Sunderland 0
Sunderland, England - Manchester United did its part on Sunday as Wayne Rooney's first-half goal was enough for United to earn a 1-0 win at the Stadium of Light over Sunderland, only for City to snatch the title away in cruel fashion.
Rooney's goal came in the 20th minute from a Phil Jones cross, but the score could have been much more comfortable had it not been for the woodwork and the play of Sunderland goalkeeper Simon Mignolet.
The crossbar came to the rescue for Sunderland on a Rooney free kick, while the England striker wasted a great chance by missing the net from close range shortly before the break.
Paul Scholes hit the post in the second half for United, while Rooney also hit the woodwork with a free kick as the Red Devils comfortably closed out the game.
United was ready to celebrate at the final whistle as City was still trailing, but an unbelievable finish at the Etihad Stadium denied Sir Alex Ferguson another trophy.
Arsenal 3, West Bromwich 2
West Bromwich, England - Arsenal fought back to clinch third place and a spot in the Champions League on Sunday with a 3-2 win over West Bromwich in Roy Hodgson's final game in charge of the Baggies.
Yossi Benayoun got the Gunners off to a good start with a goal after four minutes, but the hosts answered quickly as Shane Long and Graham Dorrans took advantage of some poor Arsenal defending to score four minutes apart and put West Brom in front.
Andre Santos leveled the contest on the half-hour mark, and Arsenal benefited from a goalkeeping error by Marton Fulop to snatch the win 10 minutes after halftime as Laurent Koscielny scored from close range.
Tottenham 2, Fulham 0
London, England - Tottenham will be left to sweat on its Champions League place as Spurs finished the season in fourth place following a 2-0 win over Fulham on Sunday.
Arsenal's win over West Bromwich leaves Harry Redknapp's side in fourth and has Tottenham hoping for a Bayern Munich win over Chelsea in the Champions League final next Saturday in order to book a place in the competition for themselves.
Emmanuel Adebayor scored after two minutes to put Tottenham on its way, and Jermain Defoe doubled the advantage shortly after the hour mark when he collected a deflected shot from Aaron Lennon to fire past goalkeeper Mark Schwarzer.
Chelsea 2, Blackburn 1
London, England - There was no real incentive for either Chelsea or Blackburn in Sunday's contest at Stamford Bridge as the Blues claimed a 2-1 win over Rovers.
Chelsea will have an eye toward Saturday's Champions League final with Bayern Munich and were already locked into sixth place, while Blackburn's loss against Wigan last Monday ensured the club of relegation.
Ironically, Chelsea's goals came from players who will be suspended for Saturday's final as John Terry and Raul Meireles scored three minutes apart in the first half before a second-half tally from Blackburn's Yakubu Aiyegbeni.
Everton 3, Newcastle 1
Liverpool, England - Everton closed out its Premier League campaign with a 3-1 win over Newcastle at Goodison Park on Sunday, allowing the Toffees to close out the season on a nine-game unbeaten run.
The signings of both Steven Pienaar and Nikica Jelavic in January have done plenty to spark Everton's revival, and both scored in the opening 30 minutes to put the hosts 2-0 up.
A win would have given Newcastle a chance at a top-four finish, but John Heitinga made sure the Magpies left with no points as he scored his first goal of the season before a Tony Hibbert own goal handed Newcastle its lone tally.
Norwich City 2, Aston Villa 0
Norwich, England - Norwich City's first season back in the top flight ended with a 2-0 win over Aston Villa at Carrow Road that leaves the Canaries in 12th place.
Grant Holt's 15th goal of the season came after nine minutes to put the home side in the lead, and Simeon Jackson added another in the 22nd to help Norwich snap a four-game winless streak.
Villa was better after halftime but still failed to find the net and ends the year in 16th place, only two points above the drop zone.
Stoke City 2, Bolton 2
Stoke-on-Trent, England - Bolton's 11-year stay in the Premier League came to an end after a Jonathan Walters penalty kick in the 77th minute helped Stoke City to a 2-2 draw against Wanderers on Sunday.
Bolton needed a win and a QPR loss to Manchester City to stay up, and with QPR losing in the dying moments at City, Bolton would have remained in the top flight if it could have held on to its 2-1 lead.
Walters scored after 12 minutes to put Stoke ahead, but Bolton responded with goals from Mark Davies and Kevin Davies shortly before halftime to take the lead.
However, the crucial moment came in the 77th minute when Bolton goalkeeper Adam Bogdan brought down Peter Crouch inside the area, allowing Walters to fire home the spot kick and doom Bolton to the Championship.
Swansea City 1, Liverpool 0
Swansea, Wales - A disappointing season for Liverpool came to a close on Sunday with a 1-0 defeat at Swansea City.
The result leaves Liverpool in eighth place, four points back of rivals Everton, while Swansea will be delighted with its first season in the top flight having finished in 11th place.
Swansea had the better of the play but had to wait until the 86th minute when Angel Rangel's pass picked out Danny Graham and he fired a shot beyond Liverpool goalkeeper Doni for three deserved points.
Wigan 3, Wolverhampton 2
Wigan, England - Wigan ended its season on a great run as the Latics claimed a seventh win in nine games by topping relegated Wolverhampton, 3-2, at the DW Stadium.
Wolves put up a fight in its final top-flight match and took the lead through Matt Jarvis in the ninth minute.
But Franco Di Santo canceled out the opener a few minutes later for Wigan and Emmerson Boyce tallied two goals for the hosts before a late consolation goal from Steven Fletcher, which was wasn't enough to prevent Wolves from ending the season on a 14-game winless streak.