The in-form Argentinian took his recent goal tally to eight in six games - nine for the season overall - with a quickfire double as City beat CSKA Moscow 2-1 at the Khimki Arena.
The pre-match headlines were dominated by concerns about the pitch and the post-match ones by alleged monkey chants aimed at Yaya Toure, but in the game itself it was Aguero who stole the show.
Manchester United flop Zoran Tosic put CSKA ahead against the run of play after 32 minutes but Aguero immediately equalised, digging a David Silva cross out from under his feet to touch home.
He headed a second from a fine Alvaro Negredo cross eight minutes later and City held on to move clear in second place in Group D behind Bayern Munich.
A repeat victory over the Russians at the Etihad Stadium in their next fixture should all but secure a place in the knockout stages for the first time.
Manager Manuel Pellegrini said: "It was a very important victory and (we knew) if we (were to) win, we (would) have a lot of chances to go into the next round.
"The next game is at home. We can decide if we can qualify for the next round and that is very important for us."
City had a number of chances to increase their lead after moving ahead with David Silva and Toure, twice, testing Igor Akinfeev.
Aleksandar Kolarov fired a free-kick narrowly wide, Silva lost his footing as he aimed another shot and Alvaro Negredo also had a goal disallowed for handball.
City were almost made to pay for their profligacy as CSKA finished strongly.
Keisuke Honda looked certain to equalise in injury time, with the best of their chances, but Joe Hart blocked his effort at point-blank range.
Ahmed Musa also had fine strike ruled out for a foul as City clung on.
Pellegrini said: "Our first task is to qualify for the next round. "After that, we (want to) continue to go through to the other rounds, but we must first qualify."
After thrashing Viktoria Plzen 5-0 to maintain their 100 per cent record, champions Bayern are well on course to winning the group.
City now stand alone in second place with six points.
Pellegrini's attention now turns to Sunday's difficult trip to Chelsea in the Barclays Premier League.
"For tomorrow, we will start thinking about the next match against Chelsea," said the Chilean after the game.
"It's a very tough game, but we don't have any problems with the squad.
"Vincent Kompany and all of the other players are fit, so we are in a good shape."
Captain and key defender Kompany missed the trip to Russia to continue his recovery from a thigh injury.