The Toffees were desperate for points to avoid a relegation dogfight at the end of the season and young Rooney made an impact from the outset as he seemed to leave his mark on the game.
He linked up well with captain Duncan Ferguson to find a chink in Aston Villa's defence early on. His snap shot was easily held by Thomas Sorensen. The teenager found himself at the centre of attention again moments later.
The referee signalled for advantage despite Rooney clearly being held round the waist by Lee Hendrie. When the ball ran away from his feet, the young prodigy let his feelings known to the Villa midfielder.
The resulting pushing match had to be broken up by referee Matt Messias with a free-kick given to the visitors.
Everton's play started off well with some lovely fluid passing and stalwart Blue Steve Watson provided the inspiration down the right flank with a couple of nice moves.
And minutes later, when Rooney won a free-kick on the edge of the box, the Midlanders looked in real danger.
Ferguson snapped a quick shot at an unsuspecting Villa defence, but his effort cleared the bar by at least a foot.
A nervous David O'Leary started pacing up and down his dugout while Everton continued to pile on the pressure.
Bald defensive force Thomas Gravesen was felled in the middle of a run into the Villa half and the resulting play earned Alessandro Pistone a shot on goal, but he scuffed the chance.
At times it was hard to see why Villa are currently sitting pretty in the seventh spot of the Premiership table. They only managed to get out of their own half for around five minutes during the first period.
And Juan Pablo Angel should have punished a momentary lapse in Everton's solid defence. But the Colombian international fluffed a wide-open shot when he hooked it wide.
Rooney displayed his hot-headed nature again when he body checked Thomas Hitzlsperger on the stroke of half-time.
The rash move earned him his ninth yellow card of the season and he continued to protest his innocence with an unimpressed Messias as they headed towards the changing rooms.
Everton's fans let them know they would settle for nothing less than a win with a chorus of boos which rang out at the whistle. The Blues responded by coming after the break with a renewed fervour to score.
Gravesen gave the home side something to cheer about with some fancy footwork which nearly broke Hiltzperger's ankle. He left the Villa man floundering on the floor in his wake, but the cross was broken up by the head of Gareth Barry.
The Merseysiders managed to keep most of the action in Villa's half, but too often their over-laboured build-up play resulted in nothing but frustration.
Desperate to break the deadlock, manager David Moyes substituted Watson for Tomasz Radzinski in the 67th minute.
And just when it seemed nothing was going to go Everton's way after Radzinski hit the bar with a well-taken header, the super sub scored ten minutes after taking the field.
A clever run by Rooney, which saw him hop over a sliding challenge from Hendrie, left him open on goal.
But his quick vision spotted Radzinski storming unmarked into the box and his perfectly weighted cross simply bounced off the Canadian's head and into the back of the net.
Villa's floodgates were then opened and Everton's unlikely hero was Gravesen just six minutes later.
The great Dane made a determined run past three Claret shirts and drilled a low shot across the goal and past a bewildered Sorensen.
The much-needed three points will take the pressure off a care-worn Moyes, who credited his team's perseverance and he gave particular praise to Gravesen.
He said: "The boys really deserved the victory, all through the game they really kept at it.
"The points we got in the past two months haven't reflected our performances on the pitch.
"It was a big relief to finally get the win and Tommy particularly played very well and shrugged off a poor first half to finish strong."
Man of the Match: Wayne Rooney - The 18-year-old star was influential throughout the match, creating most of Everton's chances. Despite picking up yet another yellow card for an unnecessary challenge, he kept the spark going when some of his team-mates looked ready to surrender.