Mitchell Johnson (2-45) and Shane Watson (2-58) also chipped in with the ball but Australia's spinners were very expensive, with Xavier Doherty (0-41 off five overs), David Hussey (0-34 off five) and Steven Smith (0-15 off two) all receiving treatment from Sri Lanka's batsmen.
Australia's batting didn't get off to a great start with Malinga removing Shane Watson (5) before debutant Shaminda Eranga (2-38) clean-bowled struggling Brad Haddin (5) in his first over of one-day international cricket.
Ricky Ponting (22) showed some poise before Eranga deceived him with a clever slower ball and when Malinga removed captain Michael Clarke (46) the run chase was in trouble at 4-123.
Hussey attempted to save things with Steve Smith (18), but when the latter was run-out brilliantly by an instinctive Nuwan Kulasekara and the former followed a ball later caught at point off Malinga the writing was on the wall.
There was still time for Dinesh Chandimal to complete a spectacular one-handed catch to remove Johnson (1) to send the home fans into raptures.
The series now moves on to Colombo with game four to be played on Saturday.
- AAP