The 21-year-old, on his first Premier League start, escaped punishment from referee Mark Halsey for the knee-high challenge which resulted in the Magpies defender being carried off on a stretcher but Whelan believes it was an accident.
"The ball was there and McManaman got the ball as clear as a whistle, then followed through and they collided," he told BBC Radio 5 Live.
"The referee was 15 yards from the tackle. I don't think his view was blocked. He had a clear view. I had a clear view in the stands.
"He hasn't gone over the ball. That's an accident. There is not one ounce of malice in [him].
"He is an enthusiastic young boy. He has got great prospects. He was very upset by it all."
The Latics chairman had his leg broken in the 1960 FA Cup final while playing for Blackburn and the injury cut short his career.
"When I broke my leg in the cup final it was exactly the same type of tackle," he added.
"We both went for the ball. It brought back memories. It ruined my career. I am not going to criticise Norman Deeley.
"These things happen in football. He came over the ball but he didn't do it with the aim of breaking my leg."