"Of course we're in a good position but it's still wide open," said Puel, now without Argentine striker Lisandro Lopez who scored twice but picked up a yellow card and will be suspended for the return leg next Wednesday.
"We will miss Lisandro and they will get Alou Diarra back. That counts," he told reporters.
"They gave us a hard time tonight and will do that again next week. Everything's still to play for."
Bordeaux played extremely well, coach Laurent Blanc said, but paid a heavy price for uncharacteristically poor defending.
"First of all I want to say I saw a very good match, and I mean a very good match from Bordeaux," the Girondins coach told reporters.
In their previous eight Champions League games this season Blanc's side had conceded three goals, a tally doubled after the end-to-end Lyon encounter.
"I saw lots of good things, collectively and individually, from us tonight," Blanc said.
"What was maybe not so good was the fact that we were nervous at the back," added the former France defender, who was missing injured central defender Marc Planus and suspended holding midfielder Diarra.
"If you look at our defence tonight, we had young players who lack experience for that kind of match and it showed," Blanc said.
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