Earlier, Lukas Podolski and Milivoje Novakovic each scored twice as Cologne beat Mainz 4-2 for its fourth straight win at home.
Cologne climbed out of relegation trouble to move to 13th place, while Mainz drops to fifth.
Hannover took the lead against the run of play in the 26th with Ya Konan’s 11th goal of the season. The Ivory Coast striker beat a weak challenge from Mikael Silvestre to reach Jan Schlaudraff’s cross, before firing low across goal past Sebastian Mielitz.
"It came out of the blue," said Werder coach Thomas Schaaf.
Hannover has never lost a game in which Ya Konan has scored.
Mertesacker rose high above Karim Haggui to equalize with a header shortly after the interval, sending the ball into the bottom right corner.
Marko Amautovic went close with a shot from 22 meters (yards) five minutes later as Werder continued to attack.
Ya Konan – already on a yellow card – was lucky to escape another when he knocked the ball forward with his hand with half an hour remaining.
Both sides pressed for the winner and Mielitz produced an impressive save in the 80th to deny Lars Stindl in a one-on-one after a great through ball by Schlaudraff.
The Bremen goalkeeper produced an even better save three minutes later, when he rushed out to take the ball away from Schlaudraff’s feet.
Hannover goalkeeper Ron-Robert Zieler made a mistake with five minutes remaining when he carried the ball outside the area but Marin blasted Werder’s free kick high.
Manuel Schmiedebach cut down Marin with an ugly challenge around the final whistle, leading to angry confrontations at the end.
"The team has shown that it wants to win. The desire is there, the enthusiasm is there. That says something to me," Schaaf said. "I can’t blame the team."
Podolski opened the scoring for Cologne in the third minute, when his free kick from 35 meters (yards) was missed by Martin Lanig and bounced before ending in Heinz Mueller’s net.
Sami Allagui equalized in the 31st but Cologne restored the advantage in the 43rd. Heinz Mueller made a stunning save from Lanig’s header off a free kick from Christian Clemens, only for Novakovic to knock in the rebound from close range.
Podolski scored his ninth goal of the season in the 55th, when Slowomir Peszko capitalized on an error by Nikolce Noveski and squared the ball to Podolski who beat two defenders before rounding the goalkeeper.
Novakovic equaled his strike partner’s tally five minutes later, when he eluded three defenders to slot the ball past Mueller.
Podolski was given a standing ovation when he was substituted late in the game, before Petar Sliskovic got a late consolation for Mainz in the 89th.
"When we go forward, apply pressure and attack, we can play good football," Podolski said. "But we’re not yet where we want to be."