Dimitri Seluk accused the City manager of “humiliating” Toure, 33, by leaving him out of the club’s Champions League squad at the start of this month.
The Ivorian midfielder, who announced his retirement from international duty on Tuesday, has not figured in a single City match-day squad since then.
“The day after that, his agent spoke and in that moment, Yaya is out,” Guardiola told a press conference.
“Unless Mr Dimitri Seluk comes back to the press or to his friends in the media – because he hasn’t the courage to call me, he goes to the media – and apologises to Manchester City first of all, then his teammates and afterwards the trainer.
“When that happens, Yaya will be part of the group and he will have the chance to play.”
Toure has recovered from a migraine that made him unavailable for Saturday’s 4-0 Premier League win over Bournemouth, but he will not be considered for Wednesday’s League Cup tie at Swansea City.
Seluk had said: “If he (Guardiola) wins the Champions League for City this season, then I will travel to England and I will say on television that Pep Guardiola is the best manager in the world.
“But 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.”
In response to Guardiola’s remarks on Tuesday, Seluk said he would only apologise if the City manager said sorry to both his predecessor Manuel Pellegrini and outcast goalkeeper Joe Hart.
“I will apologise to Guardiola if he will apologise to Pellegrini for what he did to him,” Seluk told Sky Sports News.
“If you are a gentleman, this just does not happen. He signed a new contract last year then he gets pushed out for Guardiola to come in. Pellegrini was a gentleman.
“Guardiola also needs to apologise to Joe Hart. It’s not right to come to England and then get rid of a few English players.
“Guardiola wants a new future for Yaya, for Hart, and they won’t be the last.”
Toure, who is in the final year of his contract at the Etihad Stadium, has featured just once for City since Guardiola’s arrival.
He played the full 90 minutes of their Champions League play-off second-leg victory over Steaua Bucharest in August.
Guardiola added: “I cannot accept as a coach that every agent, when his player doesn’t play, goes to the media and speaks.
“I know how much Dimitri Seluk loves Yaya Toure. If he loves him, show me by apologising to Manchester City for what he said in the papers.”
Guardiola said that, as a player at Barcelona in the early 1990s, he would never have dared to allow his agent to speak out against Dutch legend Johan Cruyff, then the club’s manager.
“I cannot imagine in my day when a player’s agent would go to the media and speak against Johan Cruyff,” he said.
“Maybe it’s the new era, but I’m from the old generation, and an old-generation agent has to make his players his job and the coach his job.
“Today agents believe they are more than they are. If you have a problem, we can talk. Until he speaks, Yaya isn’t going to play.”
Toure has been at City since 2010 and has won two Premier League titles, two League Cups and one FA Cup during that time.
While Toure will play no part at Swansea, captain Vincent Kompany could return, having not played since April after undergoing groin and thigh surgery.