Armstrong, aiming for his third consecutive title, remained in third place in the overall standings. The Texan finished third in Saturday's prologue, an individual time trial in Dunkirk.
On a gray and windy day, Zabel completed the 120.78-mile circuit between St. Omer and this northern port city in 4 hours 55 minutes 15 seconds.
Armstrong registered the same time as Zabel but was well back in the pack, which grouped 161 of the 188 riders.
Christophe Moreau of France, the prologue winner, finished 31st but retained the yellow jersey. Armstrong is four seconds behind.
Armstrong, whose U.S. Postal Service team is being investigated by a French judge following allegations of illicit practices at last year's Tour de France, did confirm a relationship between him and controversial Italian sports doctor Michele Ferrari, who is due to appear in court in September charged with doping offenses.
Ferrari is charged with prescribing banned substances to professional cyclists, including erythropoietin, or EPO, which boosts endurance by increasing the number of oxygen-carrying red blood cells.
"He has never discussed EPO with me and I have never used it," Armstrong said in a statement he released through his U.S. Postal Service team.
Ferrari has assisted Armstrong's U.S.-based training advisor Chris Carmichael in a "limited role" because Carmichael cannot be in Europe--where Armstrong mostly races--on an ongoing basis.
Armstrong, 29, who recovered from testicular cancer in 1996, said he'd been working with Ferrari to attack the hour record set by Chris Boardman last year. Boardman covered 49.442 kilometers (30.9 miles) in an hour at the velodrome in Manchester, England.