Barca, whose Primera Liga lead has been cut from 12 to seven points in the last two weeks, were under sustained pressure from the seven-times Ligue 1 champions in the opening stages of their first knockout round first leg tie on Tuesday.
Karim Benzema missed a couple of gilt-edged chances for Lyon before Thierry Henry's diving header from a corner midway through the second half cancelled out Juninho's seventh-minute opener.
Barca failed to sparkle at the Gerland stadium and have now gone three matches without a win, after drawing with Real Betis and losing to Espanyol.
"It's just that we were a bit worn out," Ivory Coast midfielder Yaya Toure told reporters. "We needed a bit more time to recuperate after Saturday's game.
"It is a long season and we had to play some 60 minutes with 10 men against Espanyol at the weekend," he added, referring to Seydou Keita's 38th-minute red card at the Nou Camp.
NOT EASY
"We are playing in all competitions and at this stage of the season it is not easy from a physical point of view."
Barca were without dependable left back Eric Abidal, who suffered a groin injury on Saturday, and influential midfielder Andres Iniesta (thigh strain).
Lionel Messi, who has not scored in Barca's last five games, was also kept quiet by France defender Jean-Alain Boumsong.
"Did we eventually wear them down ? No, because we did not score a beautiful goal as we often do in the Liga," Henry told reporters.
"Before, Barca would not score a lot from set pieces. But this season we have been working on that a lot and it paid off."
Toure was confident his team would be ready for Sunday's league game at Atletico Madrid.
"We have some time to recuperate and our performance in Lyon is encouraging. It's good for the Atletico game," he said.
