Rooney struck twice in three minutes right after the restart, ensuring United survived a nervy finish after Luis Suarez had pulled a goal back.
However, with Suarez refusing to shake Patrice Evra's hand before kick-off, the off-field problems which have scarred this rivalry over the past few months have merely continued.
Evra reacted angrily and after apparently trying to confront Suarez in the tunnel at the end of the first half, celebrated victory in close proximity to a disconsolate Suarez.
The Uruguayan continued to walk down the tunnel as some of Liverpool's players took umbrage at Evra's celebrations, remonstrating with the defender as tempers threatened to boil over.
Amid the rancour, United emerged with three precious points.
The game got stuck in a midfield scrap until the final minute of the half, when Rio Ferdinand sent Suarez to the deck with a tackle TV replays showed was perfectly legal. Suarez felt differently and when referee Phil Dowd refused to award the free-kick he reacted furiously.
Booting the ball towards the dug-out as the half-time whistle blew, Suarez had to be escorted down the tunnel by team-mates. But Evra confronted the Uruguayan and players from both sides were involved in a melee that required police intervention.
Straight after the break Rooney swept home Ryan Giggs' curling corner and the home fans barely had time to catch their breath before the striker struck again. This time Antonio Valencia found the United man, who finished off his 17th Premier League goal of the season.
Suarez forced the ball home after United's defence had got themselves in a tangle, while David de Gea saved superbly to deny Johnson in stoppage time and United held on.
Source: PA
Source: PA