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The batsman, who hit 102 runs off 197 balls, was given out lbw when Broad's delivery hit the knee, and it was a perfect start for the bowler as he kicked off the day with a wicket maiden.
Pakistan were able to recover as Shafiq pulled up his 50 with a four through the slips off Wood, and James Anderson was issued with two warnings for running on the pitch, meaning that a third would prevent him from bowling again in the innings.
After a spell of Pakistan dominance, Sarfraz Ahmed (32) was caught out by Anderson after sending a high ball to mid-on off the bowling of Ali, who claimed a second wicket of the day two overs later.
Wahab Riaz (6) went for a six, but Anderson was at mid-on once again to catch, giving England the momentum for the first time in the Test.
Wood called an end to Pakistan's time at the crease when Shafiq was sent packing on 83 after sending the ball straight to midwicket, where Joe Root was placed to catch.
England will open their innings with the bat after lunch.