The Omega Pharma-Quick Step team rider, a favourite for the London Olympics, posted a time of 24 minutes and four seconds over the 20 kilometre course between Turnhout and Arendonk.
The 27-year-old German, who won the time trial gold medal at the world championships in Copenhagen last September, was 46 seconds quicker than Lieuwe Westra with Martin's team-mate Niki Terpstra third.
Triple stage winner Andre Greipel was only 41st and lost the overall lead to Martin who has a 46 second advantage over Vacansoleil's Westra going into Sunday's final stage.
"It will not be easy tomorrow. I expect a lot of opposition from Rabobank, BMC and primarily Lieuwe Westra. Fortunately I do have an excellent team," said Martin who fractured his shoulder blade, upper arm and facial bones when he was hit by a car during a training ride in Switzerland last month.