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.
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.
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.
