The onrushing Reds goalkeeper denied Mame Biram Diouf what looked set to be a clear goal-scoring opportunity in the 39th minute, tripping the attacker just outside the area.
Mignolet escaped with a yellow card and the resultant free-kick came to nothing as Liverpool later turned their single-goal advantage into a comprehensive victory at bet365 Stadium.
Klopp felt the presence of retreating defenders was enough to justify the caution.
"I do not think it was lucky with Simon Mignolet. There were two defenders around the situation and he is not the last man," the German told BBC Sport.
Leading through Sadio Mane's classy early finish, Liverpool avoided what could have been a tricky end to the contest as substitute Mohamed Salah struck twice in six minutes.
The Egypt international's brace - his 11th and 12th league goals of the season - justified Klopp's decision to relegate him to the bench alongside Jordan Henderson, Philippe Coutinho and James Milner.
"Thank-you is all I said to Mohamed Salah. It is nice to come on in a situation like this," Klopp said.
"We had a lot of work to do, with Peter Crouch on the pitch it makes it difficult, and [Stoke] are good on the ground.
"But we have to keep fighting for the second ball. It was very deserved and we are very happy."