The 25-year-old German recorded a time of 7.00:78 at an average speed of 49.62 km/h to edge out long time leader and home favourite Joost Posthuma.
The Rabobank rider was eventually pushed down a further place by Discovery's George Hincapie although the top three were separated by less than a second.
It was Schumacher's fourth victory of the season following on from a double success in the Giro d'Italia and a triumph in the Circuit de la Sarthe.
Eneco Tour
Schumacher wins after crash
23/08/2006 AT 15:29
Schumacher said afterwards: "I started the race determined to do well and I knew I had chance of winning the prologue.
"I'm going to try and win the race overall because the course suits me. The stage four time trial around Landgraaf and the final stage to Ans in Belgium seem made to measure for me.
"Of course there are still seven stages to go and anything can happen because there are a lot of other potential winners."
Belgian world champion Tom Boonen underlined his power over short distances against the clock by taking fifth place in 7.04:46.
He will be the favourite to land Thursday's first stage, a 176.9km trek from Wieringerwerf to Hoogeveen which is the first of two stages on flat Dutch roads that will suit the sprinters.
Eneco Tour
David Kopps it
22/08/2006 AT 15:10
Eneco Tour
Hincapie sitting pretty
22/08/2006 AT 11:32