The Argentine striker, opting to take the spot kick which he himself had earned, slotted the ball hard and high past Lukasz Skorupski to put the Citizens into the lead.
However, Rudi Garcia's side were able to pull a goal back midway through the first half, courtesy of the Giallorossi's talismanic midfielder Francesco Totti.
The Roma legend, who celebrated his 38th birthday on Sunday, was able to break through the City defence after latching on to Radja Nainggolan's through-ball, before chipping a classy effort into the far corner over and past Joe Hart.
Both sides came flying out of the starting blocks in the second half, as James Milner fired a dangerous drive into the box while at the other end, Totti blasted a rising 30-yarder which whizzed past the City post.
Roma then mounted on a dominant spell, seeing numerous efforts by Totti, Miralem Pjanic and Gervinho all come close, but Hart was impervious in between the sticks, helping his side remain level.
It was then City's turn to threaten in the latter stages of the game, as Gael Clichy's teasing ball came close to finding Aguero in the middle, before David Silva blasted an effort wide.
Despite both sides probing forward, no more goals were to come, and the game duly finished as a draw, with both teams sharing the points.
The result means that Man City are now third in Group E.