All eyes were on Cook at the start of the day and he responded emphatically to questions over his place in the side with a gutsy 110 at the Brit Insurance Oval.
But just as England began to entertain ideas of setting up a match-winning lead, Mohammad Aamer and Saeed Ajmal bowled a devastating spell to leave the hosts 221-9.
The pair ended with four wickets apiece as England limped to a slender lead of 146 before bad light stopped play.
England's selectors and players have been unwavering in their support of Cook but there was a sense that he needed a major score here to justify their continued faith.
At 6-1 and 69 runs behind it was a tense starting point and, despite middling one to the midwicket boundary, the pressure soon mounted.
Mohammad Asif twice located the left-hander's outside edge in the fourth over of the day but there were early signs that the luck, for once, was with Cook.
Both balls drew an indecisive prod from the batsman but each dropped short of the cordon and squirmed to the boundary.
Nightwatchman James Anderson hit one crunching cover drive before Ajmal removed him with a loosener and Cook was again fortunate when a thick edge off Wahab Riaz flew between slip and gully.
Riaz then rapped him on the pads just before drinks but did not call for what could have proved an awkward review.
After that Cook began to settle and, with Jonathan Trott happy to surrender the strike, he moved through the forties with some sumptuous work through the covers.
The scores were level by the time Cook reached 49, with a single taking England into the lead and earning the batsman a warm round of applause from a full house.
By now he looked a different player, attacking good length balls and hammering Riaz for four past backward point to bring up the 50 partnership.
The afternoon session began under murky skies but there was little movement through the air for Pakistan's bowlers.
Asif persevered regardless and almost had Trott playing on with 21 to his name.
Cook was hitting his stride at the other end, cutting Ajmal for a pair of fours in the 42nd over.
That brought him to 97 and all that was required to see him to a 13th Test century was a firm defensive prod to Asif, who obligingly hurled the ball high over Cook's head for four lamentable overthrows.
When the end came it was a soft one, tickling a legside delivery from Riaz to Kamran Akmal, but his innings was one of genuine substance.
That brought Kevin Pietersen to join Trott – who had contributed only 25 to a 116-run stand with Cook.
Pietersen briefly fired before tea but despite a smattering of boundaries his 23-run offering was unsatisfactory.
Ajmal ended his stay with the sixth ball after the break, Pietersen lunging unsuccessfully at one that spun sharply to hit off stump.
Trott was next to go, slicing Aamer to gully having made 36 in a painstaking three-and-a-half hours.
Now five down, England's 120-run lead suddenly looked worryingly flimsy. Paul Collingwood did little to help the situation, lasting only 10 balls before flashing at Aamer and feeding Kamran Akmal a third catch.
Eoin Morgan joined the post-tea procession when the tireless Ajmal forced a delivery through his defences to bowl him for five.
Matt Prior looked impenetrable in his first-innings 84 not out but could not match that this time, instead adding only five more runs to the total and one more wicket to the rampant Aamer's tally.
Graeme Swann missed with a grossly ambitious reverse sweep off Ajmal, who promptly bent back his fellow spinner's middle stump to pick up a fourth wicket.
The umpires withdrew the players as the light faded, to inevitable boos, with Pakistan firmly in the ascendancy going into day four.
Cook was understandably upbeat about his own efforts, but conceded: "It was obviously tough for us in the last session when those conditions came in. It got quite dark under the floodlights and they bowled very well with the reversing ball that spun too.
"A lot of credit goes to Pakistan but it's disappointing to lose six wickets.
"But these things happen, we're 150 ahead and we'll try to eke that out in the morning and hopefully put them under pressure when we bowl."
Of his century, he said: "When your top score in a series is about 20 that demonstrates things aren't going as well as they might have done.
"When you are playing for England there's always pressure and when you don't perform that multiplies a lot. To respond like that today was very satisfying and showed some character.