Maxwel Cornet's double looked to have put Lyon in pole position in Group F heading into the final matchweek, with Aymeric Laporte having cancelled out the winger's 55th-minute opener.
But just two minutes after Cornet's second, City responded again – Aguero rising highest to head home from a corner and punish the hosts for some wasteful first-half finishing.
And thanks to Shakhtar Donetsk scoring a late winner against Hoffenheim, Lyon's battling performance did not prove enough to secure progression just yet, with a draw still required from their final group fixture in Ukraine next month.
6 – Sergio Aguero has scored in his last six Champions League away games – only Cristiano Ronaldo (12) has ever had a longer such streak in the competition. Pack. #LYOMCI— OptaJoe (@OptaJoe) November 27, 2018
Cornet was heavily involved from the off, missing the target with a close-range header before turning provider for Memphis Depay, who failed to connect with what should have been a simple finish.
Lyon's dominance continued, Cornet squandering another golden chance when he sliced over from six yards with the goal gaping before hitting the crossbar with a spectacular volley.
Cornet would not be denied again, though, picking out the top-left corner with a curling strike from the edge of the box 10 minutes into the second half.
Lyon's lead was short-lived, the impressive Laporte on hand to head home from David Silva's flick seven minutes later, only for Cornet's low finish under Ederson to put the hosts back ahead nine minutes from time.
But it was Aguero who had the final say when he met Riyad Mahrez's corner, directing a wonderful header into the bottom-left corner to secure a share of the spoils.
What does it mean? Lyon still with work to do
Shakhtar's last-gasp victory means Lyon must avoid defeat on matchweek six to join City in the knockout round. As for Pep Guardiola's side, a draw at home to Hoffenheim will be enough to top the group.
Dominant Ndombele goes from strength to strength
Despite Cornet's double, it was Tanguy Ndombele who really stamped his authority on proceedings from Lyon's perspective, denying Silva the space to operate. If the 21-year-old's form continues, it will not be long until one of Europe's elite clubs come knocking.
Mahrez, Sterling go missing
Guardiola attempted to match Lyon's system by utilising Mahrez and Raheem Sterling in free roles, but the pair rather got in each other's way.
Key Opta Facts
- After failing to get out of the group in their first two Champions League campaigns, Manchester City have reached the knockout stage in each of their last six participations in the competition.
- Lyon are unbeaten in their first five group-stage games in the Champions League for the first time since 2008-09.
- City's Sergio Aguero has scored in each of his last six Champions League away appearances – only Cristiano Ronaldo (12) has embarked upon a longer such streak.
- Lyon's Maxwel Cornet has scored in both of his Champions League appearances versus City (3 goals).
- David Silva has provided more assists for City in the Champions League than any other player (9).