Earlier Pakistan had won the toss and chose to bat first in the first of the two-match Test series in Dubai.
Pakistan had beaten Australia 2-0 in their last Test series in the UAE in 2014.
If an lbw appeal shows the point of impact between the stumps and pads is more than 2.5 metres, an umpire's decision can not be overturned.
Australia have only won on three occasions in Test cricket after conceding at least 482 runs in the first innings.
Lyon looked risky early with debutant Marnus Labuschagne appearing to chastise himself after failing to get his hands on a half-chance at bat-pad.
The part-time legspinner struck minutes before tea, removing Asad Shafiq (80) with a ripping delivery which caught the right-hander's edge.
Pakistani batsman Haris Sohail was allowed to remain at the crease after the video review deemed the ball had hit the pad more than three metres down the pitch.
Lyon finished with figures of 2-114 after toiling for 52 overs in the punishing heat.
Resuming overnight at 3-255, both Sohail and Shafiq batted resolutely with Australia captain Tim Paine delaying the second new ball until lunch with Pakistan moving to 4-329.
"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.
Peter Siddle's early wicket of nightwatchman Mohammad Abbas propelled the 33-year-old ahead of Merv Hughes as Victoria's most prolific Test paceman and the ninth-most successful Australian quick with 213 dismissals.