The tourists won the first One-day match on Friday by seven wickets but Pakistan 'A' levelled the series in the second on Sunday, cruising to victory by eight wickets.
Phil Jacques cracked a brilliant 114 and Cameron White a quickfire unbeaten 59 in Australia 'A's total of 273-7 in 50 overs in the decider.
Pakistan 'A' were shot out for 176 in 39 overs with Test batsman Bazid Khan topscoring with 95.
Pakistan had won the two-match Test series 1-0 earlier this month.
Australian chairman of selector Trevor Hohns described the Australia 'A' tour as "one to spot future talent" in the aftermath of Australia's upset Ashes defeat to England earlier this month, their first for 18 years.
Nielsen, head coach of the Australian cricket academy, said his boys got the competition they needed.
"The tour provided us the much needed competition, quite exactly what we asked for, and proved that we have quality players to get elevated to the Australian national team," he said.
Australia have drafted 'A' team players James Hope, Brad Hodge and Nathan Bracken for their squads for next month's Super series against the World XI.
The tourists fly out late Tuesday night.