Rodri underwent surgery for the injury earlier on Friday, Guardiola said.
"Surgery this morning, ACL and next season he will be here. This season is over," Guardiola told reporters. "Unfortunately we got the worst but these things happen. We will be there to support him in his recovery step-by-step."
The Spaniard injured his right knee during the team's 2-2 draw with Arsenal in the Premier League on Sunday.
Guardiola's team top the table on 13 points ahead of Saturday's clash at Newcastle United.
The injury is a cruel twist, coming days after Rodri warned of strike action by players over their increasing workload.
Rodri is considered a favourite to win the Ballon d'Or after leading City to an unprecedented fourth straight Premier League title and then was named EURO 2024 player of the tournament.
"What he gives us, we don't have a similar player. But the others can all together replace what Rodri has given since his arrival to us. We will have to do it as a team and find a way to play a lot of matches without an important player for us," Guardiola added.
Rodri appeared to jam his knee in the 21st minute at the Etihad Stadium on Saturday, and looked in considerable pain while he was treated on the pitch before limping off.
City will also be missing midfielder Kevin De Bruyne on Saturday after he went off injured at halftime in their Champions League game against Inter Milan last week.
Rodri is among numerous players and managers who have spoken out about the jam-packed game schedule due to the expanded Champions League and FIFA Club World Cup formats, alongside enlarged national team competitions.
