The 21-year-old utility forward caused controversy with his challenge on the Magpies left-back during the game at the DW Stadium on Sunday, which saw him avoid any form of caution
The incident itself, which saw the left-back stretchered from the pitch with what is feared to be a serious knee ligament injury, went unpunished by referee Mark Halsey and his match officials.
With Latics boss Roberto Martinez admitting after the game that it was a poor challenge before defending McManaman's character, Whelan has gone even further with his take on the controversial matter.
"Young McManaman went in for the ball and got the ball, as clean as a whistle, then followed through and they collided," the Wigan supremo 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 was very upset by it all."
Wigan went on to beat Newcastle 2-1 courtesy of a late winner from Arouna Kone as they bid to preserve their top-flight status for another year.