Malinga (4/43) became the fourth bowler to pick 50-plus wickets in World Cup history as Dhananjaya de Silva (3/32) and Isuru Udana 2/41) played the support cast role brilliantly.
For England, Ben Stokes remained not out on 82 off 89 balls, his fighting innings laced with seven fours and four sixes, as he tried hard to stage a miraculous comeback with No. 11 Mark Wood (0) but in the end, fell short as Wood nicked Nuwan Pradeep (1/38) to the wicketkeeper in the 47th over.
England were 186/9 with 47 runs still to get when Wood joined Stokes in the middle. Stokes did brilliantly well to not expose him in Malinga's last over and then smashed Udana for two consecutive sixes in the 46th over to hit two back-to-back fours off Pradeep in the next.
Trusting Wood would block the last ball of the over, Stokes took a single but as it turned out, the fast bowler could not stave off the Lankan surge as the 1996 champions erupted in joy. The 35-year old Malinga is now the second Sri Lankan after Muttiah Muralitharan (68) to join the club a" with Glenn McGrath (71) and Wasim Akram (55) being the other bowlers.
With the victory, Sri Lanka moved to fifth place with six points from six games while England remained third with eight in their kitty from six outings.
Chasing a modest 233 for victory, England kept losing wickets at regular intervals from the beginning with Malinga creating havoc and keeping the Lankans in the game.
Jonny Bairstow was trapped in front for a golden duck in the only the second ball of the innings, with fellow opener James Vince (14) also failing to make an impact Malinga had him caught behind.
Reduced to 26/2 inside the first seven overs, Root and skipper Eoin Morgan tried to steady the ship with a 47-run stand but Isuru Udana took a stunning return catch off his own bowling to send England's last match's hero back in the hut for 21.
The big moment of the game came in the 31st over when Malinga got Root's back with a caught behind which was confirmed after Sri Lanka asked for a review.
Root, who was expected to anchor England's chase, looked to guide the ball down to fine leg but got a faint edge, as reviews showed, to wicketkeeper Kusal Perera.
Jos Buttler (10) did not last long, getting out leg before wicket to Malinga as England were in all sorts of trouble after de Silva scalped two wickets of Chris Woakes (2) and Adil Rashid (1) in the 41st over to swing the tide in their favour.
It was all downhill from there before Stokes almost did the jugular but fell short in the end.Earlier, Wood and Joffra Archer attacked in a pair as England restricted Sri Lanka to 232/9 in 50 overs.ABoth pacers picked three wickets each and while Archer gave away 52 runs in his 10 overs, Wood bowled 8 and conceded 40.
For Sri Lanka, Angelo Mathews top scored with an unbeaten 85 off 115 balls.Sri Lanka never really got going in the innings. They lost their first wicket in the second over of the innings, bowled by Archer.
Captain Dimuth Karunaratne was done by a delivery that was bowled in the channel but moved away from him. It took Karunaratne's edge as it went to the wicket-keeper and Archer got his first wicket of the day.
Woakes then got Kusal Perera in the next over and Sri Lanka found themselves 3/2. Sri Lanka then managed to not lose any more wickets in the first 10 overs with Avishka Fernando looking in control.
Fernando hit six fours and two sixes before a lose shot off Wood in the 13th over went straight to Adil Rashid at third man and he had to walk.
Angelo Mathews and Kusal Mendis then laboured on with a 71-run stand for the fourth wicket. However Rashid then got a twin strike, dismissing Kusal and Jeevan Mendis off consecutive balls and Sri Lanka found themselves tottering at 133/5 at the 30-over mark.
Mathews then got steady assistance from de Silva which ensured that Sri Lanka crossed the 200-run mark. Archer and Wood then ran through the lower-order and ensured that the mighty England batting line-up have to chase a target below 240.
Brief score: Sri Lanka: 232/9 in 50 ovs (Angelo Mathews 85, Avishka Fernando 49; Mark Wood 3/40); England: 212 all out in 47 overs (Ben Stokes 82 not out; Joe Root 57; Lasith Malinga 4/43)
( With inputs from IANS )