Premier League - Manchester United win 19th league title
Rooney converted nervelessly to equalise on 73 minutes after Paul Robinson had brought down Javier Hernandez.
Brett Emerton had given Rovers a 20th-minute lead at Ewood Park as Steve Kean's men produced a tireless team performance that gave the new Premier League champions a real fright.
Next weekend's season finale at home to Blackpool now offers Ferguson the chance to rest some players ahead of the Champions League final against Barcelona. He can also take satisfaction in the fact he has not only knocked Liverpool off their perch, but also upstaged neighbours Manchester City's participation in the FA Cup final.
United finish the season having won just five of 19 away games in the Premier League, but made a decent start. The visitors enjoyed copious possession, and might have led on four minutes when Nani's header shook the crossbar following a Rooney cross.
However, Rovers came into it, making more of their scant possession and nearly going in front through Christopher Samba, who sliced a volley over on 11 minutes.
Twice in the first half Kuszczak was extremely lucky to escape unpunished after dawdling on the ball and getting caught in possession.
But there was no reprieve when he went walkabout in search of a chip from Emerton that scooted to the left-hand side of the box.
Though Kuszczak returned to his goal, the goalkeeper's impromptu excursion visibly unsettled a defence that left Emerton unmarked to sweep the ball in left-footed when it came back into the area.
Hernandez and Rooney showed some good interplay, but Rovers closed down ferociously, denying United time on the ball. Phil Jones and Samba put their bodies on the line, while Michel Salgado hassled Nani to distraction.
Hernandez nearly converted a half-chance when he wrapped his left-foot around the ball 25 yards out and brought a good save from Robinson, but otherwise United chances were at a premium.
Blackburn continued their memorable rearguard action into the second half, prompting Ferguson to sacrifice a defender, Fabio, when he brought Paul Scholes off the bench.
But Rovers continued to pose a threat, and Jonas Olsson rattled the woodwork with a header that gave Kuszczak no chance.
United's moment finally came when Hernandez chased a long ball down the left channel and touched the ball just before Robinson upended him.
Referee Phil Dowd consulted his linesman as both sides surrounded him, then pointed to the spot, satisfied that contact has taken place with the ball still in play.
It was a good decision, and a rash piece of goalkeeping from Robinson, with Hernandez running the ball out for a goal kick.
After Rooney found the corner of the net, the latter stages were something of a damp squib, with both sides happy to settle for a point - though wins for Blackpool and Wolves mean Rovers are not safe yet.
United got the job done despite a sub-par performance - the perfect metaphor for a season in which they have rarely sparkled, but emerged as deserving champions thanks to their determination and consistency.