After missing several first-half chances, Maxwel Cornet finally got his goal 10 minutes into the second half, seeing a curling shot deflect off Oleksandr Zinchenko and in, but Aymeric Laporte levelled seven minutes later with a close-range header.
Cornet then restored Lyon’s lead late on (81), however just after 2 minutes, City responded again – Aguero rising highest to head home from a corner and punish the hosts for some wasteful first-half finishing.
“We are so delighted and so happy,” Guardiola said. “It is a big compliment for the team.
“We played one of toughest teams we’ve ever faced. They are physical, strong, they counter-attack incredible.
“People say the French league is just PSG, but they are so wrong.
“Always in my career when I play against French teams, they are so physical. That’s why they’re World Champions. They all have quality, they don’t lose the ball, they’re so strong and they’re fast.
“We reacted after 1-0 and 2-1 and we are in the final stages. This was our target.
“Now we must try to get a point to finish first in the group stage, but it is so important to go through.
The result means City can secure top spot in Group F if they just avoid defeat against Hoffenheim at the Etihad on matchday six.