His fellow opener Imam-ul-Haq was a lot more aggressive in his knock of 76, as the first-wicket pair added 205 runs after Pakistan captain Sarfraz Ahmed won the toss and opted to bat on a dry wicket at the Dubai International Cricket Stadium.
Australia named three debutants with batsmen Aaron Finch, Travis Head and Marnus Labuschagne coming into the team for the visitors' first test since the ball-tampering incident.
Yasir looms as a major weapon for Pakistan with the pitch already showing signs it is beginning to deteriorate. Last time Australia played three debutants in the same Test was quite recent at Adelaide against South Africa in November 2016 - Matt Renshaw, Peter Handscomb and Nic Maddinson.
Marnus Labuschagne came to Australia's rescue by inducing an outside edge off Shafiq's bat to finally put an end to a frustrating 150-run partnership.
"I get the massive honour and privilege, to present Trav with your baggy green mate", Lyon started.
"We've fought really well for two days. obviously great to get a wicket but mainly just to do the most for the team and to find a way to keep getting wickets".
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After resuming their first innings at the overnight score of 255/3, Pakistan lost night-watchman Mohammad Abbas (1) early.
Sohail was on 51 when he advanced down the crease and padded away a Lyon delivery, prompting an appeal which umpire Richard Illingworth dismissed.
Lyon looked risky from his first ball with Marnus Labuschagne appearing to chastise himself after failing to get his hands on a half-chance at bat-pad.
Lyon finished with figures of 2-114 after toiling for 52 overs in the punishing heat.
"I would've taken it after four overs, so I'm about an hour-and-a-half out", former Test batsman Mark Waugh said on Fox Sports.
An early Peter Siddle breakthrough was the only highlight of the day, bowling nightwatchman Mohammad Abbas on day two.