Bayern played for almost an hour with an extra man after Valencia's Antonio Barragan was sent off in the 33rd minute but trailed 1-0 until Thomas Mueller's 82nd minute equaliser.
The draw was enough to secure a spot in the next round for both teams after BATE Borisov slumped to a 2-0 home defeat to France's Lille, but Bayern CEO Karl-Heinz Rummenigge sought more from the Bavarians.
"We have to wake up," he told players and guests at a post-game banquet in the early hours of Wednesday.
"We have to rediscover the form that made us so strong this season and that gave us a big, big lead in the Bundesliga."
Bayern, eight points clear at the top of the Bundesliga with 10 wins from 12 matches, were held to a surprise 1-1 draw by lowly Nuremberg on Saturday.
They could have grabbed all three points against the battling Spaniards but for a string of squandered chances, while the woodwork denied Mario Mandzukic a goal late in the game.
"This was not a game for which we should celebrate," Mueller told reporters. "We had an extra player for 60 minutes but were trailing by a goal until the 82nd. It was frustrating not to have won this game. At the end it was just damage control."
Bayern have every reason to sound the alarm bells ahead of a busy week with three league games on the menu.
They host Hanover 96 on Saturday before travelling to Freiburg in midweek and then entertain champions Borussia Dortmund in a game that could see their lead cut even further and reignite the title race.
Bayern squandered an eight point-lead midway through last season to end trophyless for the second straight season, and with that implosion still fresh in their minds, Rummenigge urged the team to focus.
"We have to throw in everything we have for this coming week," said the former Bayern striker. "We have to do it to avoid what happened to us last year.
"We still have a wonderful lead but now comes a week that is hugely important for our future."