The Russian champions, beaten 3-0 by already-qualified Malaga in their group opener two months ago, conceded two goals in the space of two minutes early in the game to find themselves deep in trouble.
Diego Buonanotte opened the scoring from close range in the eighth minute before Seba took advantage of an errant pass by Zenit keeper Vyacheslav Malafeyev to fire into an empty goal a minute later.
"We got the point we needed and the squad responded in the way we wanted," Malaga coach Manuel Pellegrini told Spanish TV.
"I am very pleased with the players who had a chance to show what they can do against a great team like Zenit, who have players of great quality.
"I am very pleased to have topped the group and to have been able, more or less, to give some players a rest ahead of our La Liga match [at home to Valencia] on Saturday.
"We played a very good first half but their early goal in the second lifted their spirits. We had a few chances to get a third goal but we couldn't manage it."
"It's very hard to come back when you are two goals down after just 10 minutes," Danny told Russian television NTV Plus.
"But we tried, we did our best, we missed many chances in the first half. We scored twice after the break and could have added a third but just ran out of time."
Zenit's preparation for the Malaga game had been hampered by turmoil surrounding their league match at Dynamo Moscow, which was abandoned last Saturday after the Dynamo goalkeeper suffered an eye injury from a firecracker thrown by visiting fans.
Luciano Spalletti's team could be handed a 3-0 defeat and a hefty fine from the Russian FA.
