Lyon dismissed Azhar Ali (15) caught and bowled in his fourth over, and next ball had Haris Sohail caught close to the wicket for nought.
While Australia are confident about Starc pulling through the rest of the Test match, they are unlikely to take a risk with his involvement in the T20Is especially with a home series against India fast-approaching.
Azhar Ali has thrown away his wicket with one of the most baffling and embarrassing run outs in recent cricket history. Australia trail Pakistan by 262 runs with eight wickets intact.
Australia cricketer Nathan Lyon bowls during day two of the second Test cricket match in the series between Australia and Pakistan at the Abu Dhabi Cricket Stadium in Abu Dhabi on October 17, 2018.
Fakhar said Pakistan were in the driving seat.
The tourists' culprits with the bat were many, but in particular another failure from Shaun Marsh has intensified debate about the veteran's place in the Australian Test team, with former teammate and Australian batting great Mike Hussey acknowledging that pressure was building on his fellow West Australian.
England have often been on the rough end of Australian aggression, an approach which culminated in three players, including captain Steve Smith, being banned following the ball-tampering scandal in South Africa. Lyon was gone for two moments later, with Starc the last man out for 34, completing a five-wicket haul for Abbas.
Meanwhile Pakistan captain Sarfraz Ahmed resumed his position behind the stumps having been in some doubt after play on Tuesday having hurt his arm when struck by a Mitchell Starc bouncer late in his innings of 94. Abbas dismissed Siddle to take his 50th Test wicket.