Portugal international Guerreiro tapped in a cutback from Thorgan Hazard after Erling Haaland had failed to connect in the 32nd minute, and Hakimi fired in from a fine Jadon Sancho assist in the 78th to make sure of the three points.
The result lifted Dortmund to 57 points, one behind Bayern, who are in action against Eintracht Frankfurt later on Saturday. The Bundesliga resumed last week with no fans, after more than two months of suspension due to the COVID-19 pandemic.
Dortmund next face Bayern on Tuesday in a game that could go a long way to deciding the championship.
Wolfsburg, who suffered their first defeat in eight league games, were left with 10 men when substitute Felix Klaus was sent off for a rough challenge.