Wood finished with three for 39 and Ali fetched three for 108 as Pakistan, resuming at 282-4 lost their last six wickets for 96 runs in the extended two-and-a-half hour session due to Friday prayers.
Asad Shafiq was the last man out as he tried to heave Wood and was smartly caught at mid-wicket by Joe Root after scoring 83.
He hit nine boundaries off 178 balls and valiantly attempted to reach his century as he was running out of partners.
Misbah, who had not added to his overnight score of 102, reviewed Australian umpire Paul Reiffel's decision but the replays showed the ball was hitting the leg-stump.
Misbah hit eight boundaries and five sixes during his 197-ball stay at the crease.
Shafiq added 52 with Sarfraz Ahmed (32) before Ali struck twice by having Ahmed and Wahab Riaz (six) caught at mid-on to leave Pakistan at 7-342.
Yasir Shah scored a quick 16 with three boundaries before he became leg-spinner Adil Rashid's first wicket in the match, caught in the slip by Ben Stokes.
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