The left-arm seamer, who took three for 48 and was named man of the match, restricted the tourists to six runs from the eight needed for victory as Sri Lanka levelled the series at 1-1.
Australia, set 246 to win, were on course for a 2-0 lead after a 148 run second wicket stand between Matthew Hayden (93) and Ricky Ponting (69). But they were restricted to 244 for five with Andrew Symonds and Michael Bevan falling short in the last over.
Sanath Jayasuriya top scored for the hosts with 55, adding 121 in 135 balls for the first wicket with Marvan Atapattu (47).
Sri Lanka's middle and lower order had collapsed against the occasional left-arm spin of Michael Clarke.
Clarke grabbed career-best figures of five for 35 from 7.5 overs as Sri Lanka lost their last seven wickets for 29 runs.
Sri Lanka struck early in the Australia innings as Clarke, promoted ahead of Adam Gilchrist to counter the spinners, sliced a catch to backward point on the third ball from Vaas.
But Ponting and Hayden quickly settled and took the attack to Sri Lanka's spinners, six of whom were used during the innings.
Ponting passed 7000 one-day runs shortly before bringing up his 38th one-day fifty off 68 balls.
Upul Chandana eventually broke through in the 32nd over as Ponting top-edged a sweep to be caught at deep backward square.
Vaas took his second wicket shortly after being recalled to the attack as Damien Martyn mistimed a cover drive off a slower ball.
Kumar Dharmasena's dismissal of Hayden, caught at wide long off, brought the hosts right back into the game with Australia on 190 for four.
Hayden's 93 came from 116 balls with five fours and a six.
SYMONDS RECALLED
Andrew Symonds, on 10, was then given out leg before to Dharmasena by umpire Peter Manuel but was then called back with permission from skipper Atapattu because the ball hit bat first.
Symonds, joined by Bevan after the loss of Gilchrist, who was caught and bowled by Vaas, helped add 52 off 58 balls for the sixth wicket but the pair fell agonisingly short of the victory target.
Earlier, Jayasuriya and Atapattu had carried the attack to Australia's bowlers early on, making full use of a crucial toss.
But Australia eventually broke through thanks to an athletic stop and diving flick from Ricky Ponting to run out Atapattu.
Off-spinner Andrew Symonds trapped Jayasuriya, who had passed fifty for the 55th time in his career, lbw next over to leave Sri Lanka on 122 for two.
Mahela Jayawardene (38) and Kumar Sangakkara (39) then added 70 runs in 98 balls to leave Sri Lanka in a strong position before Clarke ran through the lower order.
Sri Lanka
M.Atapattu run out 47
S.Jayasuriya lbw b Symonds 55
K.Sangakkara c Bevan c Harvey 39
M.Jayawardene c Ponting b Clarke 38
T.Dilshan b Clarke 11
R.Kaluwitharana run out 0
U.Chandana c Gilchrist b Clarke 4
R.Arnold lbw b Clarke 10
C.Vaas c Lee b Clarke 5
K.Dharmasena run out 2
M.Muralitharan not out 2
Extras (b-1 lb-16 w-8 nb-7) 32
Total (all out, 49.5 overs) 245
Fall of wickets: 1-121, 2-122, 3-192, 4-216, 5-220, 6-225, 7-226, 8-236, 9-242.
Bowling: Gillespie 7-0-36-0 (6-w), Lee 6-0-39-0 (7-nb 1-w), Harvey 9-0-38-1, Symonds 10-0-45-1 (1-w), Hogg 10-1-35-0, Clarke 7.5-0-35-5
Australia
M.Clarke c Chandana b Vaas 0
M.Hayden c Jayawardene b Dharmasena 93
R.Ponting c Vaas b Chanddana 69
D.Martyn c Atapattu b Vaas 5
A.Symonds not out 36
A.Gilchrist c & b Vaas 0
M.Bevan not out 24
Extras (b-1 lb-7 w-9) 17
Total (for five wickets, 50 overs) 244
Fall of wickets: 1-0, 2-148, 3-170, 4-190, 5-192.
Did not bat: B.Hogg, J.Gillespie, B.Lee, I.Harvey.
Bowling: Vaas 10-0-48-3 (3-w), Dilshan 6-0-32-0 (2-w), Dharmasena 10-0-40-1 (2-w), Muralitharan 10-0-49-0, Chandana 9-0-40-1, Arnold 2-0-9-0, Jayasuriya 3-0-18-0 (2-w)
Result: Sri Lanka won by one run.
First match: Australia won by 84 runs
Third match: February 25, Colombo (d/n)
Fourth match: February 27, Colombo (d/n)
Fifth match: February 29, Colombo
