Serious questions will linger about how Australia managed to end up so far behind the game after an inspired Nathan Lyon spell left Pakistan reeling at 5-57 in the first innings.
"There are headaches aplenty for (Justin) Langer", it said, referring to the coach.
Australia were set a big target of 538 to win the second Test after some useful contributions from the Pakistan batting line-up saw them declare at 400/9.
Captain Tim Paine admitted after the loss to Pakistan that his team's batting took a step backwards during the series.
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If they let the home side play, there's no way they are coming back with anything other than gaunt faces. He added: 'I want his performance like the other players.
Southee missed the first two rounds of domestic first class cricket with a knee injury, reportedly caused by holding his baby in the same position for too long, creating a repetitive strain niggle.
Usman Khawaja is facing surgery on his knee, dealing rattled Australia a heavy blow as they face the prospect of missing their three top batsmen for the first Test against India in December. Though Mohammad Abbas was also the Player of the Series on the tour of England, here he was bowling on unresponsive subcontinent wickets in the UAE.
"Abbas is so accurate with the ball, and obviously our preparation was more spin-orientated so we've been taken by surprise by the pacer", Saker was quoted as saying by ESPNCricinfo.
Earlier, after the wicket of veteran batsman Mohammad Hafeez early in the innings, opener Fakhar Zaman and Ali put up a good partnership to steady the Pakistan innings. "Mohammad Abbas", the 35-year-old fast bowler said on Twitter. At the close of days play, Aaron Finch (24) and Travis Head (17) were at the crease with Australia still needing 491 runs with nine wickets in hand to save a 1-0 series defeat in the last two days. "The way he bowled, he was the best bowler on either side".