Prabath Jayasuriya bagged 12 in the match after Chandimal scores unbeaten 206.
At the end of the day, Kamindu Mendis (118*) and Ramesh Mendis (7*) stood unbeaten at the crease, with Sri Lanka at 431/6.
Kusal Mendis, Karunaratne lead Sri Lankan solid reply after Jayasuriya picked up six.
Sri Lanka have stayed in the game, but with batting likely to get tougher in the next few days, they might have conceded the advantage already.
Travis Head (4/10) and Nathan Lyon (4/31) destroyed Lankans in the third innings with their spin, skittling them out for 113.
The first session of play was washed out due to rain.
Lyon leads bowlers day out as Australia bowl Sri Lanka out on day one.
Kamil Mishara, Kamindu Mendis and Suminda Lakshan though failed to make the cut.
Australia beat Sri Lanka by four wickets in the fifth and final ODI in Colombo on Friday.
Charith Asalanka ton powers Sri Lanka to first series win over Australia at home in three decades.
