Stokes suffered the injury two months ago and was forced to sit out the three-match home series against Sri Lanka and the first Pakistan Test last week.
Durham seamer Matt Potts also returns to the side for the first time since the Lord's Test against Sri Lanka at the end of August.
Seamers Gus Atkinson and Chris Woakes are rested.
"Look, it's obviously got to be sensible," said talismanic all-rounder Stokes on Monday after he was declared fit, having been bowling in the nets since before the first Test.
"I'm obviously playing as a third seamer.
"I'm available to bowl and obviously when I sense the time is right for me to maybe come on and make an impact there won't be any doubts in my mind that I can come on and bowl."
Asked if he could have played as a batsman only, the 33-year-old skipper added: "Those were the sort of thoughts that went through my head at home before we came out.
"I'd written a few teams down with me not bowling, and it just didn't work."
England won the first Pakistan Test, also in Multan, by an innings and 47 runs on Friday, with Ollie Pope leading the side in Stokes's absence.
England rode on a brilliant 317 from Harry Brook and 262 from Joe Root for a stunning victory.
Pakistan became the first team in Test cricket's 147-year history to lose by an innings after posting a 550-plus total in the first innings.
England XI for second Test:
Ben Stokes (captain), Zak Crawley, Ben Duckett, Ollie Pope, Joe Root, Harry Brook, Jamie Smith, Brydon Carse, Matt Potts, Jack Leach, Shoaib Bashir
