The Argentine, who was sidelined earlier in the season with a knee injury, will miss the upcoming FA Cup clash and also potentially a key Premier League tie against the Gunners.
The Argentina international bagged his side's third of the afternoon from the penalty spot following strikes from Pablo Zabaleta and Edin Dezko, yet limped from the field just minutes later and was replaced by Carlos Tevez.
Following the victory, City assistant manager David Platt confirmed that Aguero is set to miss this weekend's FA Cup third-round tie with Watford, while the 24-year-old is also a doubt for the trip to Arsenal in the Premier League the following week.
"It’s bad enough, he won’t play on Saturday," Platt said in the post-match press conference. "Its difficult to assess an injury like that [and] how long it’s going to be. Saturday he’ll be out, and my experience would say he’d be doubtful for Arsenal."
Aguero missed a stint earlier in the season through injury, and Platt remained cautious when estimating how long the forward could be sidelined for with this latest setback.
"There's different degrees of hamstring, that’s why you need 48 hours [to assess] its not just 'It’s a hamstring and this is how long its going to be', there are different degrees of the tear that are in there," Platt said.
"It’s far too early, I haven’t got the qualities to scan his legs. There’ll be a lot of swelling in there, a bit of bleeding in there. We won’t know for 48 hours how long it’s going to be and how quick it’s going to settle down. Of course it’s a blow, but I think that’s what you run the risk of."