The skipper netted for the fourth match in a row with his side's only shot on target as Louis van Gaal's men carried out a smash-and-grab job on Merseyside.
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The opening chances of the afternoon were created by the home side when Lucas Leiva's through-ball over the top found Adam Lallana, but his header was saved by David de Gea before Roberto Firmino put the ball just wide on the follow-up.
Another fine pass opened up another opportunity for Liverpool moments later when Firmino sent a cross-field pass to James Milner, who could not steer his half-volley on target with the angle always getting tougher for him.
It was Liverpool who continued to create the chances in the opening 45 minutes, and some slick passing in and around the area opened up another one for Jordan Henderson on the half-hour mark, only for the Liverpool skipper to drag his effort narrowly past the post.
Firmino found himself in a similar position shortly before the interval at the end of a quick counter-attack, but he was thwarted by Anthony Martial's tracking just as he was about to pull the trigger.
United did have a chance to break early in the second half when Rooney and Martial found space, but the latter was quickly crowded out before he could get a shot away and soon Liverpool were right back on the front foot.
The hosts came agonisingly close to breaking the deadlock five minutes after the restart when Emre Can burst past Chris Smalling in the box only to see De Gea get just enough on his low strike to keep it out.
The visitors finally created their first chance of the match in the 56th minute when Martial showed a good turn of pace to burst past two defenders in the area before pulling his shot across the face of goal and past the far post.
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De Gea was the busier of the two keepers, however, and after gathering a Henderson effort that was straight at him, the Spanish shot-stopper once again proved his worth to United with a fine double save to deny Can and Firmino in quick succession.
Mamadou Sakho was the next to have a sight of goal, but he could not climb high enough at the back post to turn Milner's cross on target and Liverpool were soon made to pay for their missed opportunities when United grabbed the only goal of the game.
Marouane Fellaini climbed highest inside the area to plant a header against the crossbar, and the ball dropped to Rooney, who lashed home the rebound from close range past a helpless Mignolet.
It was the first time since March 2012 that Rooney has scored in four consecutive games and also took him on to 176 Premier League goals for United, making him the highest-scoring player for a single club in the competition's history.
More importantly, though, it proved to be the winning goal on the day as Liverpool fell to a fourth consecutive defeat at the hands of United.
The result lifts the Red Devils up to fifth in the league, two adrift of the Champions League places, while Liverpool remain in ninth.