At the break, Younis Khan was unbeaten on 49 and Azhar Ali was on 26, having added 62 runs for the third wicket after Pakistan won the toss and elected to bat on a flat Sheikh Zayed Stadium pitch which showed some signs of spin early on.
Younis, who scored twin hundreds in the first Test in Dubai, survived a leg-before review off Glenn Maxwell when on 35.
He has so far hit six fours during his sedate 73-ball knock.
Openers Ahmed Shehzad (35) and Mohammad Hafeez (45) were out either side of lunch.
Hafeez fell to an edge behind the wicket off paceman Mitchell Johnson.
Shehzad was shaping well during his 64-ball knock, hitting three fours before he missed a delivery from spinner Lyon and was trapped leg-before.
Australian captain Michael Clarke juggled his pace bowlers before bringing Lyon on in the 14th over to get the needed breakthrough.
Pakistan, seeking to win their first series against Australia since 1994, kept the same XI which won the first Test by 221 runs in Dubai.
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