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.
"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."
