The England forward signed a fresh £300,000-a-week deal on Friday and, after being on the periphery for much of the game, thrashed in United's second as they recorded a 2-0 win over the Eagles to move sixth in the table.
Rooney had not scored since another sweetly-hit strike in the 3-2 comeback victory over Hull on Boxing Day but he pounced six minutes after a Robin van Persie penalty to secure the points for the champions.
Manager David Moyes yet again saw his side labour in an attempt to create chances, with the attacking quartet of Van Persie, Rooney, Juan Mata and Adnan Janujaz not yielding the expected results.
Rooney saw a first-half effort cleared off the line but Palace were in the ascendancy before Marouane Chamakh's clumsy challenge on Patrice Evra on 62 minutes let United in the back door as Van Persie scored his fourth goal in five games.
Striker Glenn Murray made his first Palace start in over nine months and almost had a dream return but he could not turn home a deep cross in the second minute as Chris Smalling applied pressure at the back post.
United's first effort on goal came courtesy of Janujaz, who exchanged passes with Van Persie before firing in a shot that drifted harmlessly wide of Julian Speroni's post.
The ever-lively Janujaz had the ball in the back of the net on 17 minutes as he arrowed home a Van Persie pass but the effort was rightly struck off by referee Michael Oliver after the teenager had controlled the ball with his arm.
United were gradually starting to box Palace in without really creating any clear-cut chances to break the deadlock but it was Rooney who came close to changing that.
The 28-year-old was held up taking a corner as a Palace fan threw a coin in his direction but, after the initial delivery found its way back to his feet, Rooney clipped the ball towards goal only to see Damien Delaney head off from under his own crossbar, with Nemanja Vidic nodding the follow-up over.
Moments later it was Palace who came close for the first time as Jonathan Parr's header took a deflection off Smalling and forced David De Gea into his first save of the game.
Chamakh was the next to force De Gea into action but the former Arsenal man could only give the United goalkeeper a simple save after heading Thomas Ince's cross into the ground.
The first half then reverted back to type as the visitors bossed possession without coming close to bringing the best out of Speroni, a Rooney effort straight at the Argentinian the only save he had to make before the break.
That should not have been the case, however, as Fellaini was guilty of a poor miss, bending a left-footed shot wide after originally linking up well with Van Persie.
Rooney sent a free-kick wide in first-half stoppage time but Moyes would have been left frustrated once again at the interval as his side showed a lack of cutting edge in the final third.
Palace started the second half with a string of corners as they looked to make their visitors pay for their lack of first-half spark.
A chance finally materialised for Ince but he could only fire a difficult volley high over the crossbar before Jason Puncheon shot straight at De Gea moments later.
United were then given a simple way into a largely undeserved lead as Chamakh was guilty of a mis-judged challenge on Evra just inside the Palace box, with Oliver pointing to the spot and Van Persie sending Speroni the wrong way from the resulting penalty.
The goal seemed to rouse United from their slumber as Rooney and Mata exchanged passes before picking out Fellaini, whose low effort was well held by Speroni.
De Gea was also called upon shortly afterwards as Cameron Jerome, introduced moments before in place of Murray, curled a great effort towards goal which the Spaniard did well to push away.
United's second again came courtesy of Evra, who skipped down the left flank before crossing low to a free Rooney who drove a crashing shot into the back of the net.
Palace seemed to lose their defensive rigidity after conceding twice in six minutes and it almost got worse as Janujaz rolled in Van Persie, whose shot across Speroni came back off the crossbar.
The Eagles fought to the last to grab a consolation but slipped to just their second home defeat since Tony Pulis was appointed in November.