The ex-United midfielder defended Turkish referee Cuneyt Cakir on national television, insisting that the player should have been dismissed for "dangerous play".
However, Collins described the call as "shocking" and expressed his disappointment at Keane's remarks.
"It was a shocking decision by the referee. I was really disappointed in Roy Keane, the way he came over last night," he told talkSPORT.
"Any football player that watched that game can see Nani is only trying to do one thing and that's pull the ball out of the air.
"I felt for the United players and I felt for the team and Sir Alex. If Roy Keane was on the pitch last night he would have been raging at the referee and calling him a cheat. That's a fact."
United were leading 1-0 when Nani was given his marching orders but ended up losing the game 2-1 and bowing out of the competition 3-2 on aggregate.