The 19-year-old England star, who cost United £25million from Everton last August, again lived up to his billing as the man for the big occasion.
His two goals - one in each half - sandwiched between Gary O'Neil's equaliser, both bore the hallmark of the master opportunist.
But there is far more to Rooney. His running on and off the ball and his never give up spirit are vital characteristics in his armoury. His goals are the jewel in the crown. The first came in the eighth minute and gave United hope they could make up their inferior goal difference on both Chelsea and Arsenal.
Gary Neville curled the perfect cross from the right to the near post and Rooney raced in ahead of Portsmouth captain Arjan De Zeeuw to score with a crisp right-foot shot from eight yards.
United failed to capitalise on their early boost and Portsmouth equalised two minutes after the interval.
Yakubu Ayegbeni's run inside from the left saw United central defender Mikael Silvestre back off instead of going for the tackle.
Yakubu's shot against him rebounded to Steve Stone, whose own shot from just outside the penalty area was only cleared by Wes Brown as far as O'Neil 25 yards out.
O'Neil looked up and hit a superb curling shot which crept into the corner of the net past the despairing dive of home goalkeeper Tim Howard.
A winner looked a tall order for an out of sorts United side, but Rooney stepped forward to supply it nine minutes from time.
Ruud van Nistelrooy, starting a game for the first time in three months because of an Achilles problem, played a glorious throughball to send Rooney racing into the Portsmouth box.
Rooney's pace and power saw him shrug off a challenge from Pompey defender Dejan Stefanovic before placing his right-foot shot beyond goalkeeper Konstantinos Chalkias and into the net from six yards out.
Two-goal Rooney, named as man of the match, said: "It was a tough game and we knew it would be.
"When they equalised they made it difficult for us, but luckily we got the break. We should have been two or three up.
"I am just taking it as it comes. I have scored regularly through the season and hopefully I can keep it up.
"Ruud van Nistelrooy is one of the best strikers in the world and he played a superb ball for me to score the second goal.
"We are now six points behind Chelsea and hopefully next Saturday we will only be three points behind before they play later on that day. We still hope Chelsea will slip up."
In the context of the title race, it proved to be a case of never mind the quality, feel the points.
After Rooney's early strike, United became more and more frustrated by Portsmouth's suffocating tactics in midfield.
They missed a golden opportunity to double their lead in the 17th minute.
Rooney's shot from the edge of the Portsmouth box rebounded to van Nistelrooy and his effort was well saved by Chalkias at point-blank range.
Rooney was again the architect of another United opportunity after 39 minutes.
His diagonal run took him from the centre of the Portsmouth half to the left corner of the penalty area.
Rooney's excellent cross to the far side of the box found Gary Neville and his perfectly weighted knock back set up Christiano Ronaldo to blast his shot over the bar from eight yards.
The visitors' only chances of the first half were a weak shot wide from Yakubu and De Zeeuw's header off target in the fourth and 44th minutes respectively.
Gary Neville failed to appear after the interval after being injured in a challenge with Matthew Taylor seconds before the break and was replaced by Alan Smith.
But the home side were soon on the back foot after Portsmouth's 47th minute equaliser.
Rooney blasted a vicious 12-yard volley from the right side of the box narrowly wide in the 49th minute before substitute Ryan Giggs - on for Paul Scholes - went close with a curling 25-yard free-kick.
Rooney was near with another fierce 25-yard effort and van Nistelrooy's 75th-minute header from Gabriel Heinze's deep left wing cross was taken under his bar by Chalkias.
But, as Louis Saha warmed up on the touchline to enter the fray, Rooney struck. That was the last seen of Saha and also the last seen of Portsmouth.
After the match, United manager Sir Alex Ferguson said: "Time was running out, but we have seen this happen so many times. The determination and perseverance gets us over the line and this was one of those games.
"The pitch was a bit lively and the players were always having to take one touch.
"Wayne Rooney was by far our best player and he was absolutely magnificent. He was always taking the baton up and he proved to be brilliant.
"Van Nistelrooy's speed of pass for the second goal killed their defender. It was a terrific result for us.
"Over the years, we have seen these types of games going for the championship and it stresses the determination of Manchester United."
Portsmouth coach Joe Jordan said: "I felt we would get something out of the game. We had an awful start which we could not afford in such a difficult fixture, but we composed ourselves and did not let them create many chances in the first half.
"We got the goal which gave us belief to get out and play more attacking football. But their winning goal came from a free-kick where we went to sleep, although it was a little bit of magic."
MAN OF THE MATCH - WAYNE ROONEY
Two superbly opportunistic goals dragged a lethargic Manchester United to another win and cut Chelsea's lead at the top of the Premiership to six points.