The City boss is unhappy with remarks from Toure's adviser Dimitri Seluk, who said Guardiola was "humiliating a great player" by benching the midfielder.
"It was so difficult for me to put [Toure] out in the Champions League -- so difficult," Guardiola told a news conference on Tuesday. "I know him, I know he's a good guy, but it was difficult for me as well to put Aleix Garcia out, [they are] the only two players that are out, because the list is the list.
"But the day after his manager spoke -- in that moment -- Yaya is out. Until Mr. Dmitri Seluk comes back in the press conference, or his friends in the media, he has the courage to call me, go to the media and say an apology to Manchester City, the first one, the second one is his teammates and after the trainer.
"When that happens Yaya will be part of the group and he will have the same chance to play all the games. Because I cannot accept as a coach, every manager when his player doesn't play goes to the media and speak and speak and speak. It depends."
Seluk declined to apologise later on Tuesday, telling Sky Sports News that "I can say whatever I like and Guardiola can't stop me."
Toure has made only one appearance for City this season -- the Champions League playoff second leg against Steaua Bucharest -- and has not featured in the matchday squad for the seven other City fixtures.
The 33-year-old was also left out of Guardiola's Champions League squad -- along with Spanish youngster Aleix Garcia, who has been on the bench for City's last two Premier League games and made his debut in the 4-0 win over Bournemouth at the weekend.
And Guardiola said Toure, who also retired from international football on Tuesday, will not come into contention for Wednesday's EFL Cup clash with Swansea City at the Etihad.
"I know how Dmitri Seluk loves Yaya Toure, if he loves me, show me and make [an apology] to Manchester City [for] what he did in the [media]," he said.
"I cannot imagine in my period when I was a football player, my manager going to the media and speaking against Johan Cruyff, about this and about that.
"Maybe it's a new era now, the new period changing, but I'm an old guy. I am old generation, and old generation managers has to make his players his job and trainers his job, and today the managers believe they are more than they are.
"If he has a problem call [director of football] Txiki Begiristain, the club, and they can talk, until he doesn't speak, Yaya is not going to play."
Toure missed three days of training last week with a migraine but this week has rejoined the first-team squad.
But Guardiola will not consider him following the comments from Seluk to the Sunday Mirror in September.
Seluk said then: "If City don't win the Champions League then I hope that Pep has got the balls to say that he was wrong to humiliate a great player like Yaya."