Usman Khawaja survived to be 37 not out, although it was likely to be of little consequence ahead of Thursday’s Test squad announcement.
Left-arm paceman Shaheen Afridi earlier had Test hopeful Joe Burns caught behind on 11, two balls after he was dropped at first slip.
It was another untimely failure for Burns, who was clean-bowled by Imran Khan for a golden duck in the first innings as Australia A crumbled to be all out for 122.
Pakistan declared their second innings at 3-152 after tea, having overall handled the conditions far better than the hosts.
Iftikhar Ahmed, promoted to No.4 for the second dig, finished unbeaten on 79 and opener Shan Masood scored 65 before falling to Travis Head’s part-time spin.
Ashes reserve paceman Michael Neser (2-10) was the pick of the bowlers, trapping skipper Azhar Ali lbw and having Haris Sohail caught at gully.
Neither Azhar nor Sohail managed to compile a significant score in either innings but Pakistan will take plenty of confidence from Iftikhar and Masood having followed up on centuries to Babar Azam and Asad Shafiq in the first dig.
National coach Justin Langer and chief selector Trevor Hohns met on Wednesday to pick their 12-man squad for the first Test at the Gabba starting November 21, with none of Australia A’s batsmen having made an irresistible case for selection.