McCoy's position as second choice quarterback had come under threat from veteran Seneca Wallace, who joined the franchise on Thursday to join a battle that included Scott Tolzien and BJ Daniels as well as McCoy.
However, the 26-year-old performed well in the 49ers' 34-14 win over the Minnesota Vikings last night and Harbaugh confirmed after the match that he was happy with McCoy as the number two.
"I feel real good right now that Colt's the backup," Harbaugh told The Associated Press.
"He had a nice command of the offence. In the very short time that he's been here, he absorbed it real quick and put him in some situations where he hadn't practised some of the things he did that night.
"It showed that he was taking mental reps on the ones he wasn't in. That was real encouraging. He pays attention. He has real good physical ability and everybody likes him. He's fit in real well."
McCoy joined the 49ers earlier this season after a two-year spell with the Cleveland Browns.