United went into injury time at Sunderland leading 1-0 and with City trailing 2-1 to 10-man QPR at the Etihad Stadium.
By the time the final whistle sounded at the Stadium of Light City had levelled, but the celebrations on Wearside had barely started when Sergio Aguero saved Roberto Mancini's men at the death to clinch a first title for the Blues in 44 years.
United manager Sir Alex Ferguson and his players trudged back to the dressing room knowing they had been so close at the end of a remarkable season, but it was the home fans who stayed behind to cheer their heroes on a day when victory and defeat ultimately counted for little for either club.
United might have won significantly more comfortably on the day had it not been for the woodwork and Black Cats keeper Simon Mignolet, but they could have emerged with just a point after they failed to dispatch Sunderland with old boy Fraizer Campbell passing up a glorious opportunity to level.
For much of the opening 45 minutes, there was little doubt about how events would unfold on Wearside with the visitors dominating for long periods and creating enough chances to have held up their end of the bargain by the time the whistle sounded for the break.
In the event, they led by a single goal, courtesy of Rooney's close-range 20th-minute header from full-back Phil Jones' cross.
The England striker might have claimed a hat-trick inside 14 minutes, but he saw his free-kick come back off the crossbar on the half-hour and then uncharacteristically miskicked with the goal at his mercy four minutes later when Ashley Young's wayward shot arrived perfectly for him.
With 37-year-old Paul Scholes and Ryan Giggs, 38, running the game from midfield, it seemed only a matter of time before United increased their lead and wrapped up the win.
Mignolet had also had to beat away a well-struck effort from Giggs but as time ran down, the home side started to make an impression.
Their best chance fell to Campbell as he ran on to Stephane Sessegnon's 36th-minute cross, but to the relief of Ferguson, the man who sold him to Sunderland, he steered his volley wide of the post.
However, the mood at the Stadium of Light changed as news of City's opener started to filter around to wildly differing responses from the respective sets of supporters.
Antonio Valencia might have lifted the descending gloom for the travelling fans in injury time when he forced a decent save from Mignolet, but Ferguson's men headed for the dressing room knowing their fate was being decided elsewhere.
United returned determined to kill off the game as quickly as possible, and might have done so within two minutes when Valencia slid Rooney in only for Mignolet to deny him with a brave block.
But the fans behind the Belgian's goal were celebrating within seconds when news of QPR's equaliser sparked a delirious reaction.
Jones glanced a 50th-minute header just wide, but the home side were appealing in vain for a penalty two minutes after substitute Ahmed Elmohamady was bundled to the ground by Jonny Evans in pursuit of James McClean's cross.
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Sunderland were enjoying their best period of the game as United found themselves having to defend deep and in numbers.
But it would have been 2-0 with 59 minutes gone had Craig Gardner not thrown himself into the path of Young's volley from Valencia's teasing cross.
Young tested Mignolet at his near post with a driven cross five minutes later with the tension rising, although there were joyous scenes on the terraces when the travelling fans heard of QPR's second goal.
United were unfortunate not to increase their lead with 14 minutes regaining when Scholes smashed a volley against the foot of the post and Mignolet recovered superbly to tip Giggs' follow-up over the bar.
But as the time ebbed away, the United fans could hardly contain themselves, hoping no news from the blue half of the city was good news.
Rooney clipped the outside of the post with a last-minute free-kick and the partying was just about to start when the worst possible news arrived for those of a red persuasion.