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.
Catch all the action and live scores from Day 4 of the second Test between Pakistan and Australia through in Abu Dhabi through our live blog.
Man of the match Abbas continued his phenomenal series to snare 10 wickets across both innings as Australia fell short of their first Test series victory in Asia since 2011.
He finished the two-Tests with a total of 17 wickets which included a twin five-wicket haul in the Abu Dhabi Test and was the chief architect of their 373-run victory.
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.
Abbas took seven wickets in the first Test which Australia drew after a determined fightback on the fifth day in Dubai.
"It looks like (Australia) hadn't prepared or that they took him a little easy", Pakistan skipper Sarfraz Ahmed said after the second Test. We had some momentum from the first Test, started really well here and then from 5-57 it went a bit pear-shaped to be honest all over the field.
"But credit goes to Abbas, because the pitch is not suitable for fast bowlers", said Sarfraz.
"Abbas challenged our defence time and time again".
Head and Finch put on 61 runs for the second wicket while Starc (28) and Labuschagne added 67 for the sixth wicket, but it only delayed the inevitable.
He was struck by a cricket ball while batting on the third day of the deciding Test match. From the outfield, Starc collected the ball and threw to Australian captain, Tim Paine, who gleefully broke the stumps, to Ali's utter disbelief.