Ponting hit one six and eight fours in his 106-ball knock and skipper Michael Clarke [ Images ] made an unbeaten 58 as Australia surpassed Sri Lanka's total of 208 with more than 11 overs to spare for a 2-0 lead in the five-match series.
The duo had also scored half-centuries in their team's seven-wicket win in the previous match.
Fast bowler Doug Bollinger led Australia's disciplined attack with three wickets to restrict Sri Lanka to a modest total before Ponting and Clarke ensured victory with their 107-run stand.
Clarke, playing his 200th one-day international, hit two sixes and four boundaries in his 67-ball knock. Ponting also added 94 for the second wicket with in-form opener Shane Watson [ Images ] (43) after the early dismissal of Brad Haddin [ Images ].
Watson, who became the first batsman to complete 1,000 runs in one-dayers this year, was bowled by paceman Lasith Malinga [ Images ] after hitting one six and four boundaries in his 51-ball knock.
Former captain Kumar Sangakkara [ Images ] top-scored for Sri Lanka with a patient 52, hitting just one six and one four in his 85-ball knock. He added 63 for the fifth wicket with Angelo Mathews [ Images ] (35).
Lower-order batsman Nuwan Kulasekara [ Images ] helped Sri Lanka cross the 200-mark with a brisk 31-ball 34.
Australia gained the upper hand when they reduced Sri Lanka to 77-4, with Lee, Johnson, Bollinger and left-arm spinner Xavier Doherty taking one wicket each.
U. Tharanga c Haddin b Johnson 13
T. Dilshan b Lee 24
K. Sangakkara c Johnson b D. Hussey 52
M. Jayawardene c M. Hussey b Doherty 17
D. Chandimal c Haddin b Bollinger 1
A. Mathews c M. Hussey b Bollinger 35
J. Mendis c Bollinger b Lee 5
N. Kulasekara c Clarke b Watson 34
L. Malinga c Ponting b Bollinger 0
R. Herath lbw b Johnson 9
A. Mendis not out 7
Extras (lb-2, nb-1, w-8) 11
Total (for all out; 49.3 overs) 208
Fall of wickets: 1-37, 2-41, 3-74, 4-77, 5-140, 6-151, 7-159, 8-173, 9-195, 10-208
Bowling: Lee 10-0-50-2, Bollinger 10-2-35-3, Watson 5.3-0-29-1, Johnson 9-1-34-2, Doherty 10-0-43-1, David Hussey [ Images ] 5-0-15-1.
S Watson b Malinga 43
B Haddin c Sangakkara b Kulasekara 7
R Ponting not out 90
M Clarke not out 58
Extras: (lb-2, nb-1, w-10) 13
Total: (For 2 wickets in 38.2 overs) 211
Fall of wickets: 1-10, 2-104
Bowling: Malinga 8-0-45-1, Kulasekara 7-1-38-1, Mathews 3-0-18-0, Herath 8.2-0-57-0, A Mendis 6-0-23-0, J Mendis 3-0-12-0, Dilshan 3-0-16-0.