Wolfsburg thought they had won the game when Bosnian striker Edin Dzeko scored his second goal of the afternoon five minutes from time to give the visitors a 2-1 lead.
Mertesacker, though, rose above the Wolfsburg defence in stoppage time to head in the equaliser from a Mesut Ozil corner.
"We were not focused in defence and made it easy for our opponents," Bremen coach Thomas Schaaf told reporters.
"We had enough today chances to decide the match in our favour. But today we were lacking the right balance between offence and defence," he said.
Schalke 04, third on 25 points, missed the chance to go top when they lost 1-0 at Borussia Moenchengladbach - their first defeat since mid-September.
Hamburg failed to close in on the top when Mainz earned a 1-1 draw with an 84th minute goal from Tim Hoogland. Hamburg are in fourth place, on 24 points.
Hoffenheim are fifth, a point behind, after losing to visitors Borussia Dortmund 2-1 with a 79th-minute penalty from Nuri Sahin. The hosts were reduced to 10 men two minutes later after Maicosuel was sent off.
EARLY CHANCE
Wolfsburg keeper Diego Benaglio denied Bremen an early lead when he stopped Portuguese striker Hugo Almeida's fifth-minute header going into the top corner of his goal.
Twice more the hosts threatened with headers from Almeida and defender Naldo before Wolfsburg had a chance of their own with a shot by Brazilian Grafite.
Dzeko fired the visitors into the lead three minutes before the break when he beat three Bremen defenders inside the box and thundered a close-range shot past keeper Tim Wiese.
In-form Almeida, who had earlier missed from close range, notched up his third goal in two matches on 62 minutes when he fired in from eight metres after Aaron Hunt's backheel was saved on the line.
Dzeko then struck on the break with five minutes remaining, slotting home to put Wolfsburg back in the lead before Mertesacker headed in from close range.
Wolfsburg have won only one of their last five league matches.
