Babar Azam felt the decision to give Saud Shakeel out cost Pakistan as they slumped to a Test series defeat to England on day four at Multan Cricket Stadium.
The tourists won another dramatic match by 26 runs on Monday to take an unassailable 2-0 lead.
Shakeel (94) and Mohammad Nawaz (45) appeared to have given Pakistan the upper hand with a sixth-wicket stand of 80, but both were removed in quick succession by Mark Wood.
Aleem Dar put his finger up after Shakeel edged a delivery from Wood down the leg side and third umpire Joel Wilson stayed with the on-field decision, seeing no evidence that Ollie Pope did not take the ball cleanly.
Pakistan captain Babar believes Shakeel should have remained in the middle.
He said: "The Shakeel dismissal cost us. It looked to us as if the ball had touched the ground. As a professional, you have to respect the umpire's decision, but we felt the ball had been grounded."
England skipper Ben Stokes had a different opinion on the incident.
He said: "I don't think [there were any doubts about the catch], personally. The only thing where you start worrying is when it gets looked at for a long period of time because that's when you start having doubt in your own head.
"I've been part of games before where I've been on the team who's been on the receiving end of those decisions and you're always like, 'that's not carried'.
"You see a lot of those decisions and those type of catches in cricket. You could say the similar thing was when Rooty [Joe Root] got caught at short leg - you could say that might have touched the floor.
"But you've just got to go with what the umpire's decision is. It went our way but I've been involved in a few decisions where stuff like that has gone against us. But you can't change that."