Put in to bat by the hosts, Indians were undone by a top-order collapse and it took a fightback from the lower half to salvage the day to some extent.
Pandya was the standout performer, with his 112-ball knock that included nine fours and a six.
Jayant Yadav was the other notable contributor to the Indian scorecard with a 69-ball 28, which was laced with four hits to the fence.
For Australia Kane Richardson and Jackson Bird grabbed three wickets apiece.
Australia A captain Joe Burns won the toss and elected to bowl first under overcast conditions.
Richardson (3-37) was the pick of the bowlers early on, striking first with the wicket of Faiz Fazal (0), who edged to Nic Maddinson at second slip.
Karun Nair (1) followed, run-out by a direct hit from Hilton Cartwright to leave the tourists 2-11. The collapse that followed garnered three wickets for the home side at the expense of zero runs, leaving India A in serious trouble at 4-11.
India A captain Naman Ojha (19) fell immediately after lunch, trapped lbw by Bird to give the quick his second wicket of the day.
Ojha and Sanju Samson (13) had set about negotiating their side out of a tricky position, but the latter's innings didn't last until lunch, as Cartwright switched ends for his second over and snuck one through the batsman's defence to hit leg stump and claim a breakthrough.
The seventh wicket stand of 78 between Jayant and Pandya steadied India's rocking boat before Yadav's wicket was snared by Richardson.
Brief Scores
India A: 169/9 in 66 overs (Hardik Pandya 79 not out; Kane Richardson 3-37).