United didn't appear to be missing Rooney when Javier Hernandez and Nani scored in the first half.
But after the break, Chris Brunt's free kick went in off Patrice Evra before Somen Tchoyi tapped in from six yards after Edwin van der Saar dropped a cross from Brunt. Rooney played the last 20 minutes as United drew a third straight match.
“It's just explicable — it turned from a fantastic first half performance to one where we have given the game away,” United manager Alex Ferguson said. “We should have punished them and scored four or five before halftime.” United was third four points behind Chelsea, which has collected just four points from its last three matches.
The North London sides both rallied to win 2-1, with Arsenal beating Birmingham and Tottenham triumphing at Fulham.
Bolton also beat Stoke 2-1, while Newcastle was held to 2-2 by Wigan and Wolverhampton drew 1-1 with West Ham.
At Old Trafford, all eyes were on the star striker wrapped up on the bench as Ferguson fueled suggestions of a rift with Rooney by dropping him.
While Rooney was dealing with problems in his personal life last month, he was rested for several matches by United with the official reason being that he was struggling with an ankle injury.
But Rooney directly contradicted his manager by revealing on Tuesday that he had no fitness concerns. He had to wait until the 71st minute to come off the bench, but by that time it was already 2-2.
Hernandez pounced quickly after five minute to tap home after Scott Carson spilled Nani's free kick.
The Portugal winger gave United a 2-0 halftime lead but the Baggies hit back with their two quick second-half goals.
The result lifted United to third but it could find itself one place lower if Manchester City beats Blackpool on Sunday.
At Emirates Stadium, towering forward Nikola Zigic put Birmingham ahead when he rose above the Arsenal defense deep in the area and met a cross from Keith Fahey to beat goalkeeper Lukasz Fabianski at his far post.
Arsenal won a penalty before halftime when striker Marouane Chamakh went down easily in the box from Scott Dann's challenge.
Samir Nasri leveled from the spot in the 41st and Chamakh put the Gunners ahead two minutes after the break.
Alex Song backheeled to Jack Wilshere and the ball was played through to the Morocco international, who ghosted past defender Stephen Carr before rounding goalkeeper Ben Foster and slotting home.
Wilshere was sent off with a straight red card minutes before the final whistle after a lunging challenge that caught Zigic's ankle.
Fulham's unbeaten record ended as Tom Huddlestone struck a hotly contested second-half winner for Tottenham.
Huddlestone's hard shot in the 64th minute was initially waved off by the linesman because William Gallas was in an offside position. But the decision was overruled by referee Mike Dean as the ball never touched the defender.
Diomansy Kamara had given Fulham the lead in the 30th and Roman Pavlyuchenko equalized shortly after the ensuing kickoff.
At St. James' Park, Fabricio Coloccini headed a goal in the fourth minute of added time to salvage a 2-2 draw for Newcastle.
Charles N'Zogbia scored twice in two first half minutes against his former club to put Wigan in control, heading in Franco di Santo's deflected cross before sending a fierce drive into the top corner.
But Newcastle substitute Shola Ameobi headed in his first league goal of the season in the 72nd to start the comeback.
There was also a stoppage time goal at Bolton, with substitute Ivan Klasnic's strike giving the home side the three points, but there was still time for him to receive a second yellow card to be dismissed.
Lee Chung-yong's 25-meter (yard) goal put Bolton ahead, but Rory Delap leveled with his first goal in more than a year.
In a basement dogfight at Molineux, Mark Noble saved goalkeeper Robert Green's blushes as he scored a second-half penalty to salvage a 1-1 draw for West Ham against Wolves.
Gree failed to clear a routine corner and allowed Matt Jarvis to tap into the net.
Noble then leveled after Kevin Foley fouled Victor Obinna in the Wolves penalty. Both teams occupy the bottom two places with six points each.
