The Belgian had drawn us level with 20 minutes to go with a sweeping effort after the Maxwel Cornet's first half opener.
But a late brace from substitute Moussa Dembele ensured another gut-wrenching Champions League quarter-final exit for Pep Guardiola’s men.
And while De Bruyne admits it was difficult to break down Lyon’s stubborn rearguard, the midfielder believes he and his teammates only have themselves to blame.
“The game was open, but (Lyon) didn't really create too many chances,” he reflected.
“We need to learn - it’s not good enough. That’s it.
“The first half was not good enough and we know that, we started slow and did not have options.”
City began to grow into the game after Cornet's opener and were full value for their equaliser midway through the second half.
And even when Les Gones had regained the lead, Raheem Sterling could have hauled us level once again when his close-range effort flew agonisingly over the bar.
But while De Bruyne could not fault our effort in the home stretch, he insisted you have to take the rough with the smooth.
He said: “second half we played well, got 1-1 and had chances, but then 2-1 and 3-1 ends the game, it’s a shame for us to go out that way.
“Their keeper made a few saves and even at 2-1, we had a chance with Raz (Raheem Sterling). That’s football, fine margins make the difference.”
But our player of the year insisted the controversy surrounding Lyon’s third should not be used as an excuse.
Speaking about the decision, he said: “I’ve not seen it back, whatever they decide, they decide. I am not going to blame that, we should have done better.”
And while defeat in Lisbon will leave a bitter taste in the mouth, De Bruyne revealed one thing he can look forward to now the long haul is over.
He said: “I need to get home because my wife is expecting any moment. I have something to focus on personally. But yes, it’s hard (to take).”