Guardiola, speaking at his pre-match press conference in Rotterdam last night, simply said a “sporting decision” had been made to omit the veteran midfielder from his squad.
The City boss added that the full reason would be kept between himself and the player.
The matter raises fresh questions over the 34-year-old’s future at the Etihad Stadium.
Guardiola said: “I spoke with him and he knows the reason why, but it’s between him and me. It’s a ‘sportive’ decision.”
Toure was an unused substitute for City’s first three games of the season before being left out of the matchday squad for Saturday’s Premier League defeat of Liverpool.
It is now clear Toure was not injured.
Toure was left out by Guardiola at the start of last season, a decision which sparked a row with his outspoken agent Dimitri Seluk. That, in turn, led to a longer period of isolation from the side for the Ivorian.
That issue was eventually resolved and Toure went on to regain a place and play an influential role in the second half of the season.
Guardiola said: “Yaya was so important last season. Six players finished contracts last season and the only one who stayed was Yaya, because he is a special player.
“But the decision was he didn’t play the last game and today he was not in the squad. He knows the reason why. Hopefully he’ll play soon, but it depends on him.”
Guardiola will make a decision today on the fitness of goalkeeper Ederson.
The Brazilian has been training wearing protective headgear after suffering facial injuries which required eight stitches in a nasty clash with Liverpool’s Sadio Mane at the weekend.
Another player who will not feature is captain Vincent Kompany, who continues to be troubled by the calf injury which affected him last weekend.
Guardiola said: “Ederson is here, with protection. Today he made the training session and we will see tomorrow if he deserves to play. I have to speak with him. Vincent is in Manchester. He’s much better. I don’t know when, but he’ll be coming back soon.”
City are hoping to make a stronger showing in the Champions League this season after falling below expectations last term and exiting at the last-16 stage.
Guardiola, a two-time winner as a coach with Barcelona, made clear there is no room for complacency in a Group F campaign that begins with the Dutch champions and also features Napoli and Shakhtar Donetsk.
He said: “Tomorrow we play our first game in the group stage. It is a dream to be here again for a club like Manchester City. We fought a lot to be here because the gap was so close.
“We start our road. I know how complicated it is. Last year we were not able to win one game away.”