Rooney helped Manchester United's Under-16s to a 2-0 Premier League Shield victory on Tuesday as his parents Wayne and mother Coleen watched from the sidelines.
United lifted the trophy at Carrington after dominating Burnley and Kai was seen with a medal around his neck in a picture shared by his father on social media.
However, in a tough blow to take, Kai shared a black and white photo of himself this morning with a black and white caption.
"Disappointed to be out for the rest of the season. Back strong next pre-season.”
Kai was awarded his first scholarship within the club's youth system and will be eligible to sign a professional contract next season as he aims to push into the first team over the coming years.
He has followed his father's lead by signing with Triple S Sports Management and secured a fresh scholarship last month in what has been a dramatic rise through the ranks for the teenager so far.
Kai will now rest behind the scenes as he takes a break from the game. Rooney spoke on his son earlier this season and admitted that a lot of his game is inside his head as he deals with the mental side of football.
"He has great coaches at Manchester United, so I take a stand off approach. I speak to him, but for me, it's all about his mentality and his mindset, to make sure he keeps enjoying it - that's the main thing for me."