United ended the season on 87 points, two clear of Chelsea, who were leading through Andriy Shevchenko until Bolton grabbed an injury-time equaliser through Matt Taylor.
It was United's 10th Premier League title and 17th championship in all - one short of Liverpool's record - and they will now go for a domestic and European double when they face Chelsea in the Champions League final on May 21.
"It was a tough one alright," manager Alex Ferguson told Sky Sports.
"We had some nervous moments and when it started to rain anything can happen on the greasy surface. Then our oldest player, Ryan Giggs, 10 (championship) medals, comes on and scores, fantastic."
Everton qualified for the UEFA Cup after their 3-1 home victory over Newcastle United secured fifth place.
Birmingham City and Reading both had four-goal wins but still joined Derby County in being relegated after Fulham won 1-0 at Portsmouth to complete their unlikely escape.
There was also a remarkable game at Middlesbrough where the home side hammered Manchester City 8-1, helped by a hat-trick for Afonso Alves, in a mid-table duel.
There was nothing mid-table about the two main events as United and Chelsea began the day locked together on 84 points.
The first breakthrough came at the JJB Stadium when Wigan's Emmerson Boyce tripped Wayne Rooney in the box and double-player of the year Ronaldo calmly scored from the spot.
It was the Portuguese winger's 41st goal of the season for United and 31st in the league.
United had further reason to thank the referee soon after when he opted not to show Paul Scholes a second yellow card for a body check that could easily have ended his involvement.
In London, Chelsea suffered an early setback when captain John Terry suffered a dislocated elbow after a collision with his own goalkeeper Petr Cech. Though he was taken to hospital, the defender said he hoped to be fit for the Champions League final.
After struggling for impact in the first half, Chelsea improved after the break and Shevchenko, on as a second-half substitute, bundled them into the lead after 62 minutes.
With United's goal difference far superior the title was still heading back to Old Trafford though and they made certain of it when Giggs, on as a 68th-minute substitute, tucked in the second.
That ended the race but Bolton's late equaliser at Stamford Bridge gave United clear water in the standings.
"It was an important goal because it gave us a two-goal margin," Giggs, 34, told Sky Sports. "But I'm not bothered about (appearance) records, it's about championships.
"I've got 10 now and just hope I can win another."
