Abbas, on a slow turning pitch, again jolted the top order with four quick wickets in the first hour on day four.
Australian women's cricket team member Rene Farrell tweeted that when she grows up she wants to bowl like Mohammad Abbas.
Teammmate Yasir Shah is the fastest Pakistani to 50 wickets, reaching the mark in nine matches.
Pakistan were pegged back by Australia on the third day of the second Test thanks to this weird run out from Mitchell Starc.
Imad has been out of the Pakistan limited-overs squad since past year due to a knee problem and was also overlooked for the Asia Cup last month after failing a fitness test.
They have only lost one series - 2-0 to Sri Lanka past year - since being forced to play their home matches in UAE since 2009.
Australia's batsmen had no answers to his accurate seam bowling under cloudy conditions at Sheikh Zayed Stadium as only Marnus Labuschagne (43), Travis Head (36) and Aaron Finch (31) offered some resistance.
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Serious questions will linger about how Australia managed to end up so far behind the game after an inspired Nathan Lyon spell left Pakistan reeling at 5-57 in the first innings.
"It's disappointing. We came here to win this series and we did ok in the first Test and showed at least some fight and the style and brand of cricket we wanted to play in that second innings and then to come out and do that this Test, it's kind of like we've taken one step forward and then two steps back".
Khawaja, who did not open the batting in Australia's second innings, has sustained a meniscal tear in his left knee and will require surgery.
Abbas jolted the Australians in the seventh over of the day when he removed a solid-looking Head, getting an edge to substitute wicketkeeper Mohammad Rizwan, deputising for Sarfraz Ahmed.
Two balls later, captain Tim Paine was out without scoring while trying to leave a ball that nipped back enough and knocked over the off stump.
Pakistan's cricket selectors on Thursday named uncapped left-arm pacer Waqas Maqsood in the Twenty20 global squad for the series against Australia.