Ross Barkley netted a magnificent long-range opener for the hosts but Aguero demonstrated his finishing prowess by firing home an equaliser.
But the injury problems that have plagued the Argentina international since December returned as he hobbled off shortly afterwards, having appeared to aggravate a muscular problem in his leg while drilling his shot beyond Tim Howard.
On the back of a calf strain sustained in City's 6-3 home win over Arsenal and hamstring tweaks at Tottenham and Barcelona in January and March respectively, Aguero's departure was an uncomfortably familiar sight for manager Manuel Pellegrini.
Edin Dzeko goals either side of half-time were enough for City to assume control in the Premier League title race, even if Romelu Lukaku's 65th-minute header made for a frantic finale.
The 2011-12 champions now know victories over Aston Villa and West Ham in back-to-back home games next week will almost certainly see the Premier League trophy return to the Etihad Stadium, and Aguero took to Twitter to suggest he may play a part.
He tweeted: "Thank you for your concern. I left just as a precaution. Fortunately I'm fine, happy for the goal, the win and keeping our dream alive."
However, Pellegrini sounded a more cautionary tone when asked about his forward's latest setback during Saturday's post-match press conference.
Asked whether Aguero will play in City’s remaining fixtures, he said: "I don't know about that. We will know tomorrow after the doctor examines him.
"I don't know if it is his groin if, his hamstring - it is a muscle problem but we don't know exactly, in this moment, what it is.
"He came to me to tell me that he was feeling some strange thing in his leg and he would try to continue playing as much as he can."
Pellegrini added that he expects two-goal hero Dzeko to be fit for the Villa clash after he sustained a late knock to his shoulder, while confirming the decision to substitute Yaya Toure after 66 minutes was merely a precaution one week on from the influential midfielder's return from an adductor problem.
He said: "Dzeko, in that play when he fell down he had a problem with his shoulder. We will see tomorrow - the shoulders are very strange but I hope that he will not have any problem.
"Yaya is just coming back from a few muscle injuries so it is just a precaution."
