Manuel Pellegrini's side were at their clinical best on Wednesday, emerging 5-1 victors at Tottenham to extend their unbeaten run to 20 matches in all competitions.
City usurped Arsenal at the top of the Barclays Premier League as a result, although the three points at White Hart Lane came at a cost.
Having opened the scoring with a seventh goal in five games since returning from a calf injury, Aguero was forced off late in the first half with another muscular problem.
The 25-year-old will have the hamstring complaint assessed on Thursday and, while another spell on the sidelines could follow, did his best to remain upbeat after the match.
"I felt some pain in my right hamstring and left just as a precaution," he said on Twitter.
"My studies will tell me the degree of the injury.
"It's a pity about the injury but it's easier knowing that we are on top. I hope I get back out on the field soon to keep helping the team."
Another injury lay-off would be bad news for City, even though they proved again they can keep scoring without him.
Yaya Toure netted from the spot minutes into the second-half after Danny Rose's controversial red card, before Edin Dzeko struck soon after.
Substitute Etienne Capoue clawed one back for Spurs but it proved a false dawn as then came goals from Aguero's replacement Stevan Jovetic and captain Vincent Kompany, who hopes to see City's top scorer back soon.
"It's bad news of course," he said. "We will have to see. We don't know how bad it is but hopefully he'll be back very soon.
"The good news is Jovetic stepped up and was the player we know he can be."
Next up for City is a clash with fellow title hopefuls Chelsea, while Spurs will look to get back to winning ways at Hull this weekend.
The 5-1 defeat emphatically ended Tottenham's unbeaten Premier League run under Tim Sherwood, who felt his side were beaten by the champions elect.
"We've played the champions today, without question in my opinion," he said.
"Unfortunately for everyone they play, they don't just score one and shut up shop, they keep coming.
"If anyone is going to win the league you want a team like this to do it because they entertain.
"It's not great for an opposition manager, believe me, but they just put you to the sword. That's how football should be played in my opinion. They've got to win it now.
"I just think these guys are on a different level to anything in the league."