The defender was taken off at half-time against Manchester United on Wednesday because he was tired having started two consecutive games after a month on the sidelines with a groin problem.
He played 78 minutes against Southampton last weekend in his first Premier League start since April - and told Guardiola he felt it was best he came off during the EFL Cup match at Old Trafford just three days later.
“Vincent didn’t play the second half because he was tired,” Guardiola said. “That was the reason why.”
Guardiola also confirmed Kompany has a future at City under his leadership.
There have been some suggestions in the media this week that the Belgian’s style of play may not be suited to Guardiola – but the manager has refuted those claims and says the club’s focus is on ensuring he makes a full recovery from the muscle problems he’s suffered over the last two years so that he can play regularly once again.
“All professional players can play in different styles, and of course he can [play in my side],” Guardiola said.
“He has a contract, no? So of course, I don’t know what is the problem.
“He didn’t play as much the last two seasons and we want to keep him safe. We want him to have the same options as his team-mates.
"We want to take care of all the players. Vincent knows his history in the last two years. We decide after what happened in Swansea to avoid it again. The injury was minimal compared to last season.
"The game against Southampton he played 78 minutes and he said he can’t play no more, and the last game was 45 minutes. We need to handle the situation until he can play 90 minutes. It was just three days after Southampton, so maybe that’s why he was tired."
Bacary Sagna, Kevin De Bruyne and Pablo Zabaleta are all recovering well from their respective injuries – but Guardiola could not confirm whether or not they will play this weekend.
“They are getting better,” he said. “Right now I cannot answer. They are getting better - but I cannot answer if they will play at West Brom.”