Frank Lampard opened the scoring with a deflected shot after 25 minutes and 18-year-old sensation Rooney followed up with one neat side-foot and a glorious 25-metre piledriver in the 38th minute before Heidar Helguson pulled one back for Iceland.
Coach Sven-Goran Eriksson made nine changes for the second half and England's reserves rose to the challenge with two goals from striker Darius Vassell and defender Wayne Bridge's first for his country.
It was England's first win since they beat Liechtenstein in a Euro qualifier in Manchester in September ending a five-game barren spell.
The first-half performance fully vindicated Eriksson's decision to scrap the diamond-shaped midfield which had flopped in Tuesday's 1-1 draw with Japan, with commanding performances from Lampard and Steven Gerrard in the centre.
Eriksson could not have dreamed of a better send-off before his squad leave on Monday for a Group B campaign which opens next Sunday against holders France and continues against Switzerland and Croatia.
His first-choice side, with the exception of rested central defender John Terry and keeper David James, showed real strength in the middle and plenty of attacking flair up front, where Rooney sparkled and Michael Owen had a goal disallowed.
PUSHING HARD
The reserves proved they are pushing hard for places, with both Vassell and Emile Heskey, who made two of the goals, doing much to silence their critics and Jamie Carragher looking impressive at the back.
The only blot on the copy book before England face the European champions in Lisbon next weekend was conceding a goal at a set-piece when Helguson headed home a corner.
Paul Scholes, without an England goal in three years, missed a sitter and Lampard sent a header wide from point blank range as Eriksson's men took the early game by the scruff of the neck.
Lampard, who now looks to have definitively replaced Nicky Butt, was rewarded for his efforts when his shot flew in off the back of Hermann Hreidarsson.
Rooney soon steered in his first after a neat run and cutback by Gary Neville and then delivered a stunner into the side of the net after Scholes knocked the ball back to him.
Eriksson said he was very pleased with the state of his squad, in better overall shape than before the 2002 World Cup in which England reached the quarter-finals.
"I think they played very well, nice goals," he told Sky Sports, talking about his second string team in the second half.
"Vassell two goals, Heskey played well, all of them did well. I think that's important when you go into a big tournament, to feel confident also that those maybe not starting the tournament are in good shape.
"We are fitter (than 2002) and we don't have any serious injuries at all."
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