The 17-year-old started Barcelona's opening three matches of the new season, making a huge impression, and he was set to be an important player for Hansi Flick's side during the German's first campaign at the helm.
However, Bernal suffered a severe knee injury against Rayo Vallecano last month, and he has since undergone an operation, with the youngster unlikely to be back before next season.
Barcelona have confirmed an adjusted contract for the midfielder, and while his deal is still running until June 2026, it includes the option of a three-year activation to take him until June 2029 when his status as an Under-19s player ends.
Barcelona confirm new contract for Bernal
"FC Barcelona and Marc Bernal have reached an agreement on an adjustment of the player's contract, which binds him to the club until 30 June 2026, when his status as an U19 player ends, with the option to three more years," read a statement on Barcelona's official website.
The midfielder's buy-out clause has also been increased to 500m to reflect his importance to the club.
"We'll miss Bernal a lot. It's surprising how quickly he learned to play in our system. What he's done is incredible and now we have to replace him with the group we have," Barcelona boss Flick told reporters last month.
Bernal's focus will now be on going through the various rehabilitation steps to put him in a strong position to return to action during the 2025-26 campaign.
The midfielder has been with Barcelona since 2014, and he featured on 31 occasions for Barcelona B before making the breakthrough into the first-team set-up at Camp Nou.