A scrappy contest at Fratton Park erupted after 77 minutes when Pompey skipper Johnny Ertl tangled with Anthony Grant on the ground, before Yassin Moutaouakil aimed a head butt at the Boro man.
Moutaouakil got away with just a yellow card from referee Chris Sarginson before Whittingham promptly substituted him and Stevenage boss Graham Westley hauled off Grant.
While Whittingham admits he did not have the best view of the clash, he accepted his midfielder was fortunate not to see red.
"We expected it, I must admit," said Whittingham. "I didn't see the full incident and it was quite close to the linesman on the far side. He saw more of it than we saw. Like any time, you just trust what the officials do is the right thing.
"In those cases where heads touch, you expect the worst - you expect a red card. We didn't want to take any risks and that's why we brought Yassin off. He has done fantastically well for us and I want him to keep playing until the end of the season.
"I haven't asked him what was said or done. We were on the opposite side of the pitch. I'll be waiting to find out and I'm sure he'll let us know what happened."
Whittingham did not feel Pompey performed to their best, but was keen to take the positives as they extended their unbeaten run to five games.
He added: "It's pleasing that we haven't conceded again at Fratton Park; that's the most important thing.
"We didn't look as sharp as we have done in the past and didn't play the ball on the floor as much as we could have done. We didn't play enough football, but we defended resolutely again."