Boonen, who also won last Friday's Tour de France Stage 6, completed the 111.5-mile route from Montpellier to Castres in 4 hours, 25 minutes and 32 seconds.
The end of the run was a sprint in which Boonen was able to edge Erik Zabel and Robert Hunter, who won Thursday's stage, by about one-half bike length. A total of 140 riders were given the same time as Boonen.
There could be a change at the top on Saturday as the Tour de France goes with a 33.75-mile individual time trial in Albi for Stage 13. The relatively short course includes two hill climbs.
The 2007 Tour de France covers more than 2,200 miles over 20 stages and the prologue. The race wraps up July 29 in Paris.