Australia were bowled out for 74, and went on to lose by four wickets.
The side's captain told Sky Sports News: "Our defence let us down more than anything. No excuse for the way we performed.
"Shot selection was poor. I understand the public wants us playing consistently. Honestly, if we played like that then the public wouldn't want to see us playing at all."
The win gives Sri Lanka a 2-1 lead in the series, with two matches left to play.