The defeat will not do any harm to the Rahul Dravid coached side as it had already qualified for the final. The win ensured that Australia A also qualified for the title clash ahead of South Africa A.
The win meant that Australia A finished on top of the table while India A came second after the round robin encounters.
Put in to bat, Australia A made a commanding 322 for six riding on twin centuries from Kurtis Patterson (115) and Nic Maddinson (118) with Varun Aaron proving to be the most expensive Indian bowler being hammered for 65 in seven overs.
India A required 9 runs off the final over and they got 6 from the first four balls. With only 3 runs required from 2 balls, Samson was holed out by Marcus Stoinis off his former Rajasthan Royals colleague Kane Richardson's delivery.
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With 3 required off the final delivery, Richardson bowled to a perfect plan as Jayant Yadav could manage only 1 run as Shardul Thakur was run-out trying to go for a second run which would have tied the match.
Pandey especially was fluent as he has been for the better part of the tournament hitting his second century.
His innings had 10 fours and three sixes -- two off leg-spinner Cameron Boyce and one off pacer Richardson.
It was the skipper's dismissal in the 47th over that turned things as pacer Daniel Worral got him caught behind.
The momentum of the innings was lost at that stage as Samson, who also hit six boundaries and two sixes, couldn't take the team past finishing line.
Australia A: 322/6 in 50 overs (Kurtis Patterson 115, Nic Maddinson 118, Shardul Thakur 2/50, Varun Aaron 1/65).
India A: 321/8 in 50 overs (Mike Pandey 110, Sanju Samson 87, Mandeep Singh 56).