Fabio Capello's troops secured their fourth successive win at the Dinamo Stadium in Minsk, having previously beaten Andorra, Croatia and Kazakhstan in Group Six.
Steven Gerrard started on the left wing but was given freedom to roam, and he opened the scoring on 11 minutes after latching onto Rooney's lay-off and steering a low, curling 30-yard shot past goalkeeper Yury Zhevnov.
Dmitry Molosh's 35-yard free-kick drew a fine save from David James, who also kept out a long-range strike from the same player before spilling an effort from Pavel Sitko, who grabbed an equaliser on 28 minutes.
Igor Stasevich's trickery in the 18-yard box left Wayne Bridge, replacing the injured Ashley Cole at left-back, on his backside and a clipped cross to the far post was headed home by Sitko.
It remained 1-1 at the interval, meaning the Group Six leaders emerged from the dressing room with some stinging words from Capello ringing in their ears.
The Italian clearly had an effect as after Rooney jinked past two defenders only to be denied a fine solo goal by the home keeper, it was 2-1 thanks to the Manchester United forward on 50 minutes.
Heskey went on a fine run down the left flank and delivered a pinpoint cross which gave Rooney the simple task of sidefooting home from close range.
Gerrard's clever throughball found Rooney in the dangerzone and his lovely dummy was followed by a clinical finish for his seventh goal in his last five games for club and country.
Capello was quick to stress the importance of team unity in his side's victory.
"I'm very happy, it was a very important game for us," the Italian said. "Belarus are a good team. We played well in the first half but in the second half we played better.
"Gerrard played well but all the players did. It is very important for us if we want to play well we have to play like a team and not as single players.
"Tonight I saw one team and that was very important for us.
"Wayne Rooney is on good form at the moment and worked hard for the team tonight, but it wasn't just him. All the players played fantastic tonight."