The afternoon session saw Amir strike twice to initiate a collapse that saw England lose four wickets for 19 runs.
Babar Azam was taken to a hospital for a scan which confirmed a fracture that will sideline him for at least six weeks.
The Day 2 of the first Test saw a quartet of Pakistan batsmen made fifties, with England dropping four catches and missing one other obvious chance
Ireland will play their first-ever Test against Pakistan from May 11-15 in Dublin.
Pakistan won the first match by 143 runs and the second by 82 runs. The three matches were all played in Karachi.
Babar Azam hit an unbeaten 97 to steer Pakistan to their highest-ever T20 total of 205-3 before bowling out the West Indies for 123.
Pakistan crushed New Zealand by 48 runs in the second T20 in Auckland on Thursday to notch their first victory of the tour over the Black Caps.
Babar Azam clobbered eleven sixes and seven boundaries, scoring at a strike rate of 384.62.
Last year, Pakistan coach Mickey Arthur compared Babar Azam to Virat Kohli, saying the 23-year-old reminds him of the India skipper at the same age.
Sylhet Sixers have enlisted the help of Pakistan pacer Sohail Tanvir to recover their floundering Bangladesh Premier League 2017 season.
Pakistan beat Sri Lanka by 32 runs in the second day-night international in Abu Dhabi on Monday, taking a 2-0 lead in the five-match series.
Azam compiled a well-made 103 from 131 deliveries, while Malik's 81 came off only 61 balls in Pakistan's total of 292-6.
Lahore's Gaddafi Stadium saw the return of international cricket.
Pakistan, sent into bat by World XI skipper Faf du Plessis, notched 197-5 with Babar Azam hitting a rapid 52-ball 86. His career best Twenty20 score had ten boundaries and two sixes.
Babar Azam has often been compared to India skipper Virat Kohli but Pakistan's young batsman said that there was no comparison between him and the Indian run-machine.
Pakistan's victory left Group B wide open, with three teams on a win apiece after South Africa defeated Sri Lanka by 96 runs at the Oval last week.
An unbeaten 85 by Azhar Ali and 55 from Babar Azam put Pakistan in a solid position at 169 for two at stumps on a rain-shortened first day of the third and final Test