As well as the defeat, Newton still feels bitter about the touchdown dance that Kaepernick did during the game in which he mimicked Newton.
The incident gained a lot of interest from commentators and fans after the game, and Kaepernick was given a lot of criticism post-game.
Newton gave his thoughts on the whole issue today when he was speaking to NFL Network.
"It's kind of a tender topic right now. Just stop talking about it right now. I don't know why he did that, but he hurt my feelings. And I think so highly of Mr Kaepernick," said Newton.
When asked about how he will respond next season to Kaepernick's mimicking, Newton said.
"You will just have to wait and see. You'll just have to tune in. There will be a response."
The interview was conducted in a joking fashion in which Newton said his comments with an off-season relaxed smile on his face.
Then all of a sudden he turned to talking about the 49ers' QB in a serious way.
"Joking aside I really respect Colin. In sports people often get caught up in the competitiveness of it. I have a lot of respect for him and Andrew Luck," he added.
"I got the opportunity to spend a couple of days with Luck during the Pro Bowl, which was great.
"I also wish RGIII a speedy recovery. Russell Wilson also, he's doing his thing at the max and I'm envious of him."