The result lifted champions United back ahead of Arsenal, who defeated fourth-placed Aston Villa 3-0 with Spain midfielder Cesc Fabregas coming off the bench to score two second-half goals, into second place.
Stuttering Chelsea faltered on Saturday when they failed to score for the first time in 34 games and were held to a 0-0 draw at Birmingham City.
Chelsea have 42 points from 19 games, Manchester United are on 40 from the same number and Arsenal have 38 but with a game in hand.
Rooney fired United ahead from close range on the stroke of halftime at the KC Stadium but allowed Hull back into the game with a woeful back pass in the 58th minute that led to a Craig Fagan penalty.
The England striker redeemed himself when his cross was turned in by Andy Dawson for a 73rd-minute own goal that put United back in front.
Dimitar Berbatov made it 3-1 by tapping in at the far post eight minutes from time, Rooney setting him up with a perfect pass. "He made a mistake in giving away the ball for a goal, that was his one bad moment in the game," said manager Alex Ferguson of Rooney's contribution. "But I thought he was exceptionally good today.
"He's a natural winner, always had a great attitude and determination to do well and he would be more sick than anyone that he made a mistake. He rectified it in a nice way," he told Sky Sports television.
Meanwhile, Tottenham Hotspur maintained their push for a Premier League top-four finish with a well-deserved 2-0 home win over struggling London rivals West Ham United on Monday.
Tottenham started at a terrific pace and took the lead after 11 minutes thanks to an electrifying burst by winger Aaron Lennon. His cut-back was half-cleared but only as far as Luka Modric, who bundled it into the net to mark his first start since August with a goal.
Spurs midfielder Tom Huddlestone hit a post 10 minutes into the second half but the home fans were getting a little nervous until a sharp counter-attack nine minutes from time ended with Jermain Defoe smashing in the killer goal at the second attempt after Rob Green had failed to hold his initial effort.
The win takes Tottenham to 37 points and back into the top four. Leaders Chelsea (42 points), who have drawn three and lost one of their last five league games, host west London rivals Fulham in the pick of Monday's later games.
"I think it's a mad league, a lot of teams are dropping points and it's really close," Rooney said after scoring a goal, giving away another and setting up two more in a 3-1 win at struggling Hull City.
"Hopefully, we can be more consistent in the second half (of the season) and retain our title."
"It's looking different, that's for sure," United manager Ferguson told Sky Sports television after his side had cut Chelsea's lead to two points.
Already this season United have been surprised by Burnley and Fulham, Arsenal have lost at Sunderland and Chelsea came unstuck at Wigan Athletic.
