Pakistan, who also had Asad Shafiq (73) to thank for digging them out of a spot of early bother, closed on 282 for six after choosing to bat and making England toil in the field for much of the day.
Yet two late wickets from Chris Woakes, who ended Thursday's play with figures of 4-45, lifted the hosts' spirits.
Misbah celebrated his landmark by dropping to the Lord's turf and doing press-ups.
"We had an army camp before the tour and every time we had to get down and do 10 press-ups. Those in my celebration can't count because my arm was bent," he said after becoming the oldest player at 42 years and 47 days to reach three figures since England's Patsy Hendren achieved the feat at 45 in 1934.
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Misbah was playing his first test in England and rode to his side's rescue, coming to the crease with Pakistan on 77 for three.
Woakes had removed Mohammad Hafeez and Shan Masood, while test debutant Jake Ball, drafted into the side in place of the injured James Anderson, trapped Azhar Ali lbw.
That brought Misbah together with the 39-year-old Younus Khan in a veteran partnership that lasted until the latter flicked a Stuart Broad delivery straight to Moeen Ali at mid-wicket for 33.
Misbah enjoyed a fine partnership of 148 with Asad Shafiq until the stand was eventually ended by Woakes three overs before the close as Shafiq edged an attempted leave behind to wicket-keeper Jonny Bairstow.
Woakes then claimed the wicket of night watchman Rahat Ali for a duck when he played on with the final ball of the day.
(Reporting by Toby Davis; editing by Ken Ferris)
