It was for the eighth time in Test cricket both the captains also kept wickets and the last time this happened was in September 2014 - Denesh Ramdin and Mushfiqur Rahim at Gros Islet.
Replays showed the ball would have clipped leg stump but the umpire's call would not have been overturned, meaning a Pakistan review would have been fruitless. Follow Australia's new home of cricket on Facebook,Twitter,Instagram and catch all the highlights, features and interviews on the 7Sport app.
Lyon looked unsafe early with debutant Marnus Labuschagne appearing to chastise himself after failing to get his hands on a half-chance at bat-pad.
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Pakistan got off to a strong start against Australia, reaching 89 for no loss at lunch on the first day of the series-opening Test match in Dubai on Sunday. The move worked immediately as the legspinner pitched one at a good channel just outside the off with the ball turning to take Shafiq's outside edge.
Lyon finished with figures of 2-114 after toiling for 52 overs in the punishing heat.
Peter Siddle, pick of the Australian bowlers with 3/58, got the lone success in the first session when he had nightwatchman Mohammad Abbas clean bowled.
Australian captain Tim Paine faced criticism for not taking the new ball until the 120th over, allowing Shafiq and Sohail to settle at the crease.
"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.