Pep Guardiola's free-scoring Premier League leaders drew a blank across 120 minutes against the Championship table-toppers but prevailed 4-1 on penalties, with goalkeeper Claudio Bravo their shoot-out hero.
The Germany international suffered a minor setback during a 2-1 win at West Brom in the Carabao Cup third round this term and has been limited to substitute cameos in the Premier League and Champions League.
After booking a quarter-final place against Wolves, manager Pep Guardiola said Gundogan "finished with some problems that hopefully will not be dangerous" and the 27-year-old confirmed it was simply a drastically increased workload leaving him running on empty.
"The last 10 minutes were really tough for me,” he told City's official website. "Fortunately, it doesn’t look that bad. I don't think I've pulled something.
"It feels like coming from zero to a hundred - 110 minutes I could handle in a very good way, but the last 10 minutes, my legs were cramping everywhere, especially in the groin."
Gundogan was undergoing rehab from a dislocated kneecap when he signed for City, while a serious back injury ruled him out of most of the 2013-14 campaign and Germany's subsequent triumphant run at the 2014 World Cup.
As the clock ticked down in Manchester against Wolves, he feared pulling up once again and took himself out of contention for the shoot-out, where Kevin De Bruyne, Yaya Toure, Leroy Sane and Sergio Aguero were on target for City.
"I was also a little bit scared that when I did a sprint something would pull," he added.
"I didn't want to leave the field and leave my team one man down, but, yeah, in the last 10 minutes I couldn't play an important part in the game.
"Normally I would also have taken a penalty but I was scared that when I shot something bad would happen."
City are five points clear at the top of the Premier League and travel to West Brom on Saturday, aiming to improve a record of eight wins and a draw from nine top-flight matches this season.