The Bundesliga's top scorer, who netted Freiburg's goal, steered the ball wide of an empty net early in the second half to waste a glorious chance to put his team ahead.
Wolfsburg notched their third successive win as they continued to recover from a terrible start to the season in which former England manager Steve McClaren's side lost their first three games.
The 2009 champions climbed to sixth with nine points from six matches, ahead of their opponents on goal difference. Mainz 05 lead the table with a maximum 18 points after Saturday's 2-1 win at champions Bayern Munich.
Hanover 96 went third with 13 points after Mohammed Abdellaoue headed the only goal in the 33rd minute, his fourth of the season, to give them a 1-0 win at promoted Kaiserslautern in the weekend's final game.
Freiburg were unhappy about both Grafite's goals, complaining that the Brazilian fouled his marker before the first while the second came from a free-kick taken from the wrong place.
Grafite put Wolfsburg ahead in the 25th minute when he headed in a free-kick taken by fellow Brazilian Diego but only after his marker Julian Schuster appeared to be pushed to the ground.
Cisse equalised 11 minutes later with his sixth goal of the season after an extraordinary sequence of rebounds, hashed clearances and misplaced passes around the Wolfsburg area.
The Senegalese should have scored again after the break when Daniel Caligiuri broke clear and laid the ball to him but Cisse missed the open goal from 12 metres.
Grafite headed in from another Diego free-kick in the 64th minute.
"The foul happened on the touchline but the free-kick was taken five metres inside the pitch," Freiburg coach Robin Dutt told reporters. "The referee made a mistake but so we did by allowing Grafite a free header."
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