City have now dropped just four points from a possible 39 from their last 13 matches in the league.
Raheem Sterling opened the scoring with a simple tap-in for his fourth goal of the season after excellent work from Leroy Sane on the left.
Sterling was also involved in City's second, exchanging a superb one-two with Aguero after the Argentine had burst forward from the halfway line, beating three players on his way.
Aguero kept his cool to slot home for the win that returned City to the top of the table ahead of the late kickoff between Chelsea and Liverpool.
He was then taken off by Guardiola, who clearly had his eyes set on Tuesday's Champions League match at Hoffenheim, which has taken on a critical importance for the Spaniard following the Lyon defeat.
"I'm a lucky guy to have this group. They are special people," Guardiola said, choosing to praise the patience and resilience of his team rather than its expansive quality.
"I was very pleased. We moved the ball quick, we didn't allow them to run at us, everybody was in the right position to move the ball quicker and our transitions are getting better, much better for instance than last season.
"The patience was important. You have to mature your game. Teams don't just defend, they defend well against us and it's not easy."
With City regaining top spot, however briefly, Guardiola added: "The important thing for us is to be solid in our game. At the top, Arsenal is coming back, Tottenham won again, Chelsea and Liverpool... the important thing is that we're focussed on what we have to do."
(Reporting by Neil Robinson and Ian Chadband,; Editing by Neville Dalton and Pritha Sarkar)
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