Australia, riding on Gilly's workmanlike 118, posted a healthy 236 on two paced wicket. In reply Lanka skittled out for 173 in 45.2 overs despite Sangakkara's defiant 80.
Sangakkara stood tall amidst Lankan batting ruins. He paced his innings to the perfection and looked set to take his side home but ran short of partners to further his cause.
Lanka, who were comfortably placed at 159/5, was undone by the disciplined Aussie attack and some shabby batting display of the Islander's top-order batters.
Pacemen Johnson and Bracken claimed three wickets each while left-arm wrist spinner Hogg took 2 for 41.
However it was Gilchrist who stole the show with his untypical but the need-of-the-hour knock.
Gilly, who will retire from international cricket at the conclusion of the series, smashed 118 from 132 balls with nine fours and three sixes to help his side post a competitive 236.
Australia at one point was cruising at 171/2 in the 37th over, lost its way, losing its last eight wickets for just 65 runs in the last 10 overs to allow the tourists nurture some hopes on a good batting wicket.
Hosts, electing to bat, lost Matthew Hayden (four) early before Gilchrist and Ricky Ponting (25) steadied innings with 50-run second-wicket stand.
Gilly was in superb touch from the word go, punishing Malinga with a series of glorious boundaries through the off-side. However he curbed his shot-making instincts latter part of the innings when wickets kept tumbling at one end.
Ponting's caught-behind mode of dismissal streak remained intact when Aussie skipper edged Chaminda Vaas straight to Mahela Jayawardene at slip, reducing Australia to 2-66 in the 13th over.
Clarke joined Gilly in the middle and consolidated the Aussie innings with 105-run stand for the third wicket. The duo paced up their innings nicely milking the ball in the gaps for singles and twos and odd boundaries.
Gilly belted Kulasekara for six in the 18th over to notch his half-century, before smashing Kulasekara for consecutive boundaries two overs later as Australia raced past 100 in the 21st over.
Clarke lost his focus when he took a blow on ribs off a scroching bouncer from Malinga. Pup fell seven runs shy of a half-century when a beauty of a doosra from Murali drew him out of the crease and Sangakkara did the rest.
Andrew Symonds (four) followed next over, reducing Australia to 177/4.
The Sydney-born Western Australian batsman's 132-ball vigil at the crease ended when a leading edge off Malinga's length ball flew straight to Kapugedara at covers with Australia at 205/5 in 43 over. And then Malinga (4/47) and Kulasekara (2/52) combined ran thro' the middle and lower-order.
Hosts will take on India in the third leg of the CB tri-series tie at Adelaide on Sunday.