Opting to bat on a placid strip, India could manage only 243 in 49.2 overs with Shikhar Dhawan (65) and Dinesh Karthik (73) being the notable contributors.
The Indian bowlers, who had been woefully out of sorts in the tournament, then managed to bowl out the Aussies for 193 in 46.3 overs to guide the team to victory at the LC de Villiers Oval.
It was India's fifth 'A' tournament victory since the concept was introduced in 1994.
Speedster Mohammed Shami (2/30) dealt initial blows to Australia 'A' and the likes of Shahbaz Nadeem (3/34 in 10 overs), Perveez Rasool (1/30 in 10 overs), Ishwar Chand Pandey (1/47 in 8 overs), Suresh Raina (1/33 in 10 overs) kept the Aussie batsmen under tight leash.
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Shami started by cleaning up rival skipper Aaron Finch (20) who went for a wild slog after hitting the bowler for a big six in an earlier over.
Glenn Maxwell (12) started with a six and four but was sent back by part-time off-spinner Raina, who opened the bowling alongside Shami. Maxwell tried to slog him past mid-wicket but was holed out to Pujara as Australia were reduced to 50 for three.
It soon became 53 for five when left-hander Nick Maddinson edged one to Raina at first slip off Pandey's bowling and Mitchell Marsh failed to beat a Rohit Sharma throw as 'keeper Wriddhiman Saha whipped off the bails in a flash.