The teenager, who boss Lee Johnson last week claimed other Sky Bet League One clubs are "frightened to death of", has scored six times since moving to Boundary Park in the summer.
He penned a 12-month contract with the option of a further year and Latics have now exercised that clause with an improved deal which will keep the former Coventry and Peterborough forward with the club until the end of next season.
"Jono's done really well since he came in," Johnson, who himself signed a contract extension recently, told the club's official website.
"When we brought him in it was a test for him to see if he could cope at this level and with our levels of intensity. He has improved a lot this year, we believe in him and that he will continue to improve.
"We felt that to give him an improved contract would show him that we value his contribution. We know that he still needs to improve but we feel that if he keeps the same attitude he has shown, he has a very good chance of having a good career."
Clarke-Harris has played in 34 games this season and is clearly relishing the extra burden placed on him.
He added: "This is a massive step in my career, I am really excited to have signed a new contract. I am really enjoying being at the club, I'm enjoying my football.
"We have a great bunch of lads here, the coaching staff have done a lot of good things for me, which are helping me to improve every day."