Alex Doolan's 104 anchored Australia's 273-8 at close on the second day at Sharjah stadium but the top-order, including Michael Clarke, did not get their much-needed practice.
Chasing 253 for a win in 50 overs, India A were bowled out for 224 in 46.2 overs with Sanju Samson's knock being the standout effort in an otherwise disappointing batting performance against Australia A.
Only 50 overs were possible on the final day before rain stopped play Australia A and India A. An unbeaten century from Phillip Hughes (100 not out) capped off the final day's play.
Doolan is expected to be available if all-rounder Shane Watson is ruled out after suffering a groin strain during the fourth Test win in Melbourne.
Graeme Smith and Hashim Amla hit unbeaten half centuries for South Africa as it warmed up for the first test against Australia in a three day match against Australia A which ended on Sunday in a draw.
South Africa tucked into some valuable batting practice ahead of next week's opening Test reaching 128 for one after the second day of their three-day tour match against Australia A at the Sydney Cricket Ground on Saturday.