The two players, aged 20 and 21 respectively, played in midfield as the French side held City to a 2-2 draw in the Champions League on Tuesday.
However, Guardiola believes Aouar, who reportedly turned down a move to Liverpool in the summer, is just as good, and was impressed with the way the pair played.
"Houssem Aouar is a very good player, he is incredible," he told reporters.
"We talk a lot about Ndombele, but Aouar is also excellent. He's always very calm with the ball at his feet, with an excellent technical quality.
"Lyon really has a very good team. There are young people full of quality and I think the team is in place tactically, I think we can congratulate them, we have had absences tonight, but we have to congratulate them!"
City are guaranteed to progress to the knockout stages of the competition after their draw, and need just a point in their final group game against Hoffenheim to confirm top spot.
And Guardiola was delighted with the way his side played, having marked Lyon out as dangerous opponents.
"We are so delighted and so happy," he told BT Sport.
"They're one of the toughest teams I have ever faced. They're physical, they're strong and their counterattacking is incredible.
"People say the French league is just PSG, but they are so wrong."
City are next in action this weekend, when they face Bournemouth in the Premier League.