Middle-order batsman Pandey cracked 13 boundaries and one six to take the visitors close to the 200-mark but once he was dismissed by Chadd Sayers, the rest of the batsmen could only score 42 runs.
At the draw of stumps, Cameron Bancroft (10) and Joe Burns (12) were at the crease with Australia A at 24 for no loss at the Allan Border Field.
Five overs later, other opener Fazal was cleaned up by David Moody. Shreyas Iyer (19) and Pandey then brought up the hundred before the 21-year-old Mumbaikar was caught and bowled by Swepson.
Pandey and newman Karun Nair (15) then added 70 runs and once the former was dismissed, Nair too could not stay longer and was sent packing by Swepson with Handscomb taking the catch.
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Brief Score:
India A 1st Innings: 230 all out in 81.3 overs (M Pandey 77; M Swepson 4/78).
Australia A 1st innings: 25-0 in 6 overs.