David Silva is available after missing the clash with Basle due to personal reasons.
Guardiola cited Spain's worldwide success with Premier League players.
Stoke went in at half-time full of heart that they might find a way back but Silva had other ideas.
The Potters are now 19th on the Premier League table, with just West Bromwich Albion behind them.
Pep Guardiola was unable to select Aguero due to a knee injury, but the Argentina star's absence was hardly noticed as City edged a little closer to the Premier League title, with Silva stealing the show.
Pep Guardiola's men thrashed the Potters 7-2 in October.
The Blues came close to increasing the lead twice in a couple of minutes as first Kevin De Bruyne very almost latched on to a poor Kurt Zouma back pass - and then the Belgian whipped in a superb free-kick that Gabriel Jesus and Nicolas Otamendi were a whisker away from converting.
Stoke have now managed just three goals in their past six games, and carried sporadic threat in a game that was effectively a free hit with no one expecting a result against the champions-elect.
And a minute later City should have gone 2-0 up when Jesus raced in at the post to meet a De Bruyne free-kick but somehow failed to make a connection.
Manchester City chairman Khaldoon al Mubarak and club owner Sheikh Mansour pictured with team manager Pep Guardiola during a visit to Abu Dhabi a year ago.
Stoke's most risky player in Xherdan Shaqiri got the better of makeshift left-back Oleksandr Zinchenko and spotted Badou Ndiaye on the edge of the box, with the Senegalese midfielder's deflected shot spinning inches wide.
Can he spring a surprise? His recent form has been fantastic, and Stoke will hope their Swiss talisman is on song once again to not just avoid a loss but perhaps, even spring a surprise on the league leaders.
City left for the airport after the Stoke game with a break in the club's owner's homeland awaiting them.
Paul Lambert introduced Peter Crouch from the bench in the 63rd minute and he made an immediate impact, heading down a free-kick to Martins Indi, who blasted over from about eight yards. It is now only one defeat in their last six games.
The Argentine was unable to add more attacking flair to a team that struggled for goals toward the end of last season under Claude Puel, and fans have recently been calling for Southampton to play two strikers up front to be more of a threat. The Hard Tackle, thus, predicts another comfortable night for Guardiola's men, who should coast to a 4-1 win on Monday.