Van Gaal said both Rooney and Anthony Martial were failing to get behind the Leicester defence and one of them was to be taken off anyway.
"No, I don't think it's an injury to Wayne. I wanted to change one of the strikers," he told the club's website (www.manutd.com).
"It could have been Martial or it could have been Rooney because they were not always running behind the central defenders, and I want that.
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"Because of this, I wanted to change but then he was limping and then the choice was easy for me to make."
United, who are third in the league, welcomed midfielder Michael Carrick back into the side on Saturday after he returned from an ankle injury suffered in England's 2-0 friendly loss to Spain.
The 34-year-old, who missed United's games against Watford in the league and PSV Eindhoven in the Champions League, thought he was set for a longer spell out of action.
"I thought it was a bad one at the time, but the scan showed that there wasn't too much damage," said Carrick. "After the swelling went down, I was free to get back involved."
United host West Ham in the league on Saturday.
(Reporting by Shravanth Vijayakumar in Bengaluru; Editing by Peter Rutherford)
