The home team were joined by the West Indies who defeated New Zealand in the Super Over during an earlier game today.
Sri Lanka piled up a score of 169 for six, the experienced Mahela Jayawardene top-scoring with 42 at the top of the order and Thisara Perera chipping in with a quick-fire unbeaten 26.
Malinga removed Luke Wright, Alex Hales and Jonny Bairstow in his first over and the chase was never really on despite late resistance from Samit Patel (67) and Graeme Swann (34).
The holders slumped to 93 for seven before Patel and Swann lifted them to 150 for nine.
"The guys played really well," Kumar Sangakkara, the Sri Lanka captain, said.
"Lasith is unbelievable, here with the new ball and with the old ball. It would be fantastic if we can win [the tournament] but the focus is to keep our feet on the ground."
Sri Lanka topped Group 1 after the Super Eight phase with the West Indies also reaching the semi-finals where they will be joined by two from Australia, India, Pakistan and South Africa, while England must head home.
Sri Lanka hit seven sixes in all, and it was clear England faced no easy task to win their last Super Eight match - as they had to if they were to qualify on net run rate ahead of West Indies.
In the event, their attempt was undermined from the outset as Malinga took a career-best five for 31 in this format.
That was not quite the knockout blow, England twice briefly threatening to put themselves back in contention. But in the end - even with a late hand from Swann to help narrow the margin - Patel was left with too much to do on his own.
"We've learnt a huge amount from this, we need to keep wickets in hand at the top, we fell short at the top of the order and are death bowling too," Stuart Broad, the England captain, said.
No Sri Lanka batsman had been able to single-handedly dominate, after being put in under the lights, Broad (3-32) faring the best of the England bowlers.
But each kept hitting big shots - and once Malinga got to work, it all proved far too much for the 2010 champions who had rarely convinced in a stuttering group campaign.
An inexperienced England line-up therefore exited, with hints of their potential if nothing more tangible, from a tournament which perhaps came too soon for several talented but still developing cricketers.
Set 140 for victory, New Zealand looked on course as Ross Taylor, the captain, led the charge with 62 from 40 deliveries.
But a late spell of tight bowling by the West Indies proved decisive in slowing the run chase, with Sunil Narine’s three for 20 the standout performance.
The match came down to the last ball with New Zealand needing two runs to win, but when Doug Bracewell could manage just one from the final delivery from Marlon Samuels, the Kiwis were left on 139 for seven and a Super Over was required.
Samuels was the hero for the Windies in the additional overs, restricting New Zealand to 17 with ball in hand before hitting the winning six after being chosen alongside Chris Gayle to face Tim Southee.
Southee’s first delivery was a no ball that Gayle smashed for six and when Samuels hit a six from the penultimate delivery the Windies had their victory.
“Marlon Samuels is my go to man in pressure situations,” Darren Sammy, the West Indies captain, said.
Taylor said: “We probably should have won it in normal time, but credit to West Indies, to score 18 off five balls is pretty awesome. When the first ball is a no ball that goes for six it ruins the over, that’s cricket and we’re going home now.”
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