Zabel, a member of the Telekom team, finished the 123.69-mile leg from Forges-les-Eaux to Alencon in 4:23:07.
"It was a great victory," Zabel said through an interpreter. "The competition in the sprint and for the green jersey is very tough this year, with world champion Oscar Freire and also Robbie McEwen. I think McEwen is the strongest sprinter. After seven or eight years on the Tour, this is a great victory."
Zabel, who turned 32 last Sunday, kept the green jersey as the best sprinter. It was the 12th career stage victory for Zabel, who was the overall leader after the third stage.
Gonzalez Galdeano took the yellow jersey after Stage Four and kept it for a third straight day. He is four seconds ahead of fellow ONCE rider Joseba Beloki.
Lance Armstrong of the United States, the three-time defending champion, remained in third place, seven seconds from the leader.
Saturday's seventh stage is 107.5 miles from Bagnoles-de-l'Orne to Avranches.