The 50-year-old man was taken into custody in the nearby town of Ratingen, police said.
He was arrested shortly after the July, 2000 bombing, but was later released for lack of evidence tying him to the crime.
At the time, the former German army solider and known Neo-Nazi ran a military surplus shop in the area and was considered a gun fanatic.
The motive for the attack is believed to be related to xenophobia.
The pipe bomb targeting the Wehrhahn S-Bahn commuter train station in Düsseldorf injured 10, mostly Jewish immigrants from the former Soviet Union returning from German language classes in the area. A pregnant woman also lost her baby.
Authorities reopened the case two years ago after using advanced DNA testing to examine a piece of railing the bomb was hung on.
cw/kms (AFP, dpa, AP)