India A captain Cheteshwar Pujara opted for batting but it took Australia 'A' only 68.5 overs to bowl out the hosts as Kohli, on whom lay entire focus, struggled badly during his hour-long innings of 16 that came off 42 balls.
In reply, Australia 'A' safely negotiated the final hour reaching 43 without loss in 13 overs with Cameron Bancroft (24 batting) and Usman Khawaja (13 batting) at the crease.
Agar in fact, got the prize scalp of Kohli with an arm ball that he failed to negotiate. It was a delivery that came straight as Kohli neither linged forward nor went on backfoot as he was struck plumb in-front.
It was a frustrating stay at the wicket for the Test captain even though he hit the other left-arm spinner O'Keefe for a straight six and got a boundary off Agar.
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Earlier, India A captain Pujara (11, 36 balls) and Abhinav Mukund (15, 49 balls) played too slowly as only 18 runs came off the first 10 overs.
It was back-up seamer Marcus Stoinis, who got Pujara out in a manner that has become familiar with the Saurashtra batsman. He was beaten by an incoming delivery that castled him.
Karun Nair (50, 153 balls, 5x4) made amends for the failure in the first match but had little support from the other end.
Naman Ojha (10) played 84 balls without much success before he lost his cool and was stumped off an Agar delivery.
Once Nair was out in the post-tea session caught by Joe Burns off pacer Andrew Fekete, the last five wickets fell for 26 runs in 11.5 overs with Sandhu wrapping up the tail.