Aussies chasing a modest 222-run victory target lost their way in the middle after a resounding start eventually succumbing to 208 in the penultimate over.
Rookie seamers Kulasekara and Amerasinghe helped Lanka turn the tables on Aussies with two wickets apiece after Gilly pyro-techniques.
Gilchrist plundered a typically entertaining 83 off only 50 deliveries but was the second man out as Australia lost six wickets in less than nine overs to slump from 113/1 in 16 overs to 123/6 in 24 overs.
Lee's brave 59-ball 37 effort proved insufficent for Aussies in the end. The Aussie pacer took the fight to rival camp in the final overs. It is shame that his rearguard action along with last man Bracken, who added 35 runs, ended in losing cause.
Any thought of a Sri Lankan victory was the stuff of fantasy while Gilchrist - clearly the aggressor in a 107-run opening stand with James Hopes, who made 28 - was in the middle.
Striking the ball as crisply as any other time during his illustrious career, Gilchrist the entertainer thrilled the MCG crowd for one last time.
After a circumspect beginning, Gilchrist threw caution to the wind. He blasted 17 from the seventh over off Amerasinghe, eight off the next from Lasith Malinga and then no looking back.
Even champion spinner Muralidaran was shown no respect as he was crashed for consecutive boundaries in consecutive overs.
Such was the might with which he was batting, the last 74 runs of Gilchrist's innings came off only 33 deliveries. It took a fine catch in the deep by Malinga to stop him.
A batsman's paradise became a minefield as Michael Clarke, Ricky Ponting and Andrew Symonds all fell in the space of 11 balls with the score frozen on 115.
Brad Haddin followed for seven in the 24th over as Sri Lanka suddenly became overwhelming favourites after being a clear underdog just 10 overs earlier.
Hogg, who was playing his last international game at MCG, failed to capitalise on start he had when he was rapped on back foot in off-stump line for a straight-forward LBW decision off Murali. Amerasinghe then accounted for Johnson's wicket caught Mahela at first slips. Lee waged a lone battle in the losing cause. His 59-ball knock was inclusive of two boundaries and a six.
Earlier, Dilshan and Jayawardene made a strokeful fifties to steer Lankans to 221 all out in 50 overs after Islanders suffered early setbacks
Mahela struck a 66-ball 50 studded with five boundary hits while Dilshan made a workmanlike 62 inclusive of three boundaries.
The duo knitted a fine 64-run stand for the fifth wicket to steady tottering Lankan ship after the much-vaunted Aussie new-ball bowlers ran thro' the top-order. The 50-run stand between Dilshan and Chamara Silva (35) for the sixth wicket also helped Lankans cause.
In-form Aussie seamer Bracken plucked 4/29 from his 10 overs after conceding just nine runs from a miserly eight-over opening spell.
After winning the toss, Lankan top order stumbled against the probing Aussie new-ball bowlers. The Islanders stumbled to 91/4 at the 25-over mark.
Mahela and Dilshan then held their ground firm and batted sensibly milking the ball in the gaps at the huge MCG for singles and twos interspersed with odd boundaries. The duo was at ease with pace but struggled against Hogg and Hopes. Hogg accounted for Mahela while Dilshan failed to beat the throw from Hopes.
Sanath Jayasuriya had a good outing in his last international on Australian soil. The man from Matara stroked a brisk 23 and dismissed the threatening Lee to steer his side home.