Early goals from David Ngog and Ryan Babel turned the game into a procession, with Maxi Rodriguez adding a third soon after half-time.
“We shot ourselves in the foot early (in the season),” Liverpool manager Roy Hodgson said, “but the limp’s getting better. Our shape was good tonight.”
The defeat means Villa have gone four games without a win and lie two places and two points above the relegation zone.
Liverpool were without Fernando Torres, who withdrew to be with his wife after she went into labour, which gave Babel his first Premier League start of the season.
Former Liverpool and England star Owen glanced in a 74th-minute header to give United a share of the points at the Reebok Stadium after Bolton had twice taken the lead through Zat Knight and Martin Petrov.
The draw saw United leapfrog Arsenal into second place in the table, three points behind league leaders Chelsea.
In a later kick-off, new Aston Villa manager Gerard Houllier’s first league match in charge of the Birmingham club saw them move up into fifth place as they won 2-1 away to Midlands rivals Wolves.
Houllier was indebted to Emile Heskey for the second time in a week as the former England striker’s late goal sealed victory after he inspired a midweek comeback League Cup win over Blackburn Rovers.
The 63-year-old – who stepped down as France coach when they failed to reach the 1994 World Cup finals – is currently employed as the French National Technical Director, which means he oversees football policy in the country.
“According to our information, Gerard Houllier has given his agreement to join the English club Aston Villa,” read the report on the L’Equipe website.
“The current DTN (National Technical Director) was in England last weekend and he left on Monday evening.
The troubled English club Aston Villa’s woes continued as they were dumped out of the Europa League with Scottish hopes also suffering a triple wipeout.
Villa, who saw Martin O’Neill quit as coach on the eve of the Premier League kick-off and James Milner sold to Manchester City, were beaten 3-2 by Rapid Vienna in their play-off second leg.
That gave the Austrians a 4-3 aggregate win to follow up their victory over the Midlanders in last season’s tournament.
Villa twice led on Thursday and also missed a penalty as they joined the Scottish trio of Celtic, Dundee United and Motherwell in being forced to write off their European hopes for another season.
Liverpool and Manchester City were left as Britain’s only representatives in Friday’s draw for the group stages of Europe’s second tier tournament.
The 58-year-old Northern Irishman announced his decision in a joint statement with chief executive Paul Faulkner on the club website (www.avfc.co.uk).
“I have enjoyed my time at Aston Villa immensely. It’s obviously a wrench to be leaving such a magnificent club,” O’Neill said.
“I pay tribute to the Villa players, my coaching staff and the Villa supporters for all the support and encouragement they have given both the club and me personally during my time as manager.”
Reserve team manager Kevin MacDonald will take caretaker charge for the club’s opening game of the season at home to West Ham United on Saturday.
Former Villa striker Gary Shaw criticised O’Neill’s decision to quit.
“I don’t know what has happened but the timing is not great. It’s a bit naughty of Martin to leave the club in this situation, just a few days before the start of the season,” Shaw told Reuters.
Rooney, who came on as a substitute for United’s other scorer Michael Owen, struck with a superbly executed header after 74 minutes, for his 20th goal in his last 20 matches, as United became the first team since Nottingham Forest (in 1989 and 1990) to win the cup in successive seasons.
Rooney, who started on the bench as he had a sore knee, told reporters: “It’s great to have this cup again, it means a lot to win a Wembley final and I am delighted to score the winner, but it’s another great day for the club and the fans.”
Aston Villa, the first winners of the trophy in 1961, and victors over Manchester United in 1994, took the lead after five minutes when James Milner scored from the penalty spot, but were often second best against a dominant United, who also hit the post twice.
Chelsea’s lead at the top of the Premier League was cut to one point on Wednesday when they lost 2-1 at Everton with Louis Saha continuing his scoring jinx over them.
Saha, who scored against Chelsea in the FA Cup final last season and in the 3-3 draw against them in December, cancelled out Florent Malouda’s 17th minute opener for Chelsea with a header in the 33rd.
He then had a penalty saved by Chelsea goalkeeper Petr Cech on the stroke of halftime before scoring the winner after 75 minutes when he chested the ball down, turned and fired home.
That sent Chelsea to their first defeat in 11 matches and gave Everton manager David Moyes his first victory over the London side on the night he celebrated his 300th Premier League game.
Chelsea remain top with 58 points, but are just one point ahead of Manchester United, who drew at Villa despite playing for more than an hour with 10 men after Nani was sent off for a ragged two-footed challenge on Stilian Petrov.