The visitors took the lead against the run of play at the start of the second half as Adrian Lopez slotted home following a quick counter-attack.
However, the home side salvaged a point in the 73rd minute as Igor Smolnikov's deflected cross looped over the head over goalkeeper Thibaut Courtois and into the net.
Here, Sports Mole takes a closer look at the action between the two teams in Russia.
On target 9
On target 4
Was the result fair?
Zenit will feel very unlucky not to have come away with the three points after dominating for long periods of the match. However, their lack of finishing gave the visitors a chance of getting something out of the game, which they did.
The Russians were in control from almost the first whistle as they hustled well in midfield while showing plenty of liveliness in attack. They would have sealed the win in comfortable fashion had it not been for their poor execution in the final third. Hulk and Aleksandr Kerzhakov in particular could have had about four goals between them were it not for some wayward finishing when it mattered. A win would have seen Zenit put one foot in the last 16, but now their fate hangs in the balance.
The Spaniards looked every bit the team that had nothing to play for as they put in a sluggish display for most of the match. Their passing, movement and general creativity was all below par, allowing Zenit to dictate proceedings. Diego Simeone's side only came alive once they opened the scoring and could have added to their tally late on. That said, they came away from Russia having avoided defeat and with their unbeaten record in this season's competition intact.
Sports Mole's man of the match
Hulk: Zenit's big Brazilian striker was a handful for the Atletico defence throughout as his powerful runs and ferocious shooting caused the visitors plenty of problems.
Atletico goalkeeper Thibaut Courtois had a moment to forget for Zenit's equaliser as Igor Smolnikov's deflected cross looped over his head and into the net when it looked as if he thought the ball was going out of play.
In what was a fiery atmosphere, Martin Atkinson did well to allow the game to be played at a quick pace and with some tasty challenges to boot.
Zenit: The Russians return to league action on Sunday with a trip to Terek Grozny.
Atletico: Madrid's La Liga campaign continues on Saturday when they travel to Elche.