The German said he was "no longer the right person" to be a part of the CCP after coming clean about his past in an interview in the Sueddeutsche Zeitung.
He admitted using banned drugs and illegal methods, including EPO, cortisone and blood doping, from 1996 until 2003.
The UCI said in a statement that Zabel had contacted the body's president on Monday to offer his resignation and to express his "deep regret for having lied for so long about taking performance enhancing substances".
Zabel was among the finest sprinters in his sport and topped the points classification of the Tour de France six times until his retirement in 2008.
He was recently named in a French Senate inquiry as a drugs offender.
Zabel featured in the French report along with several other riders including the top two in the 1998 Tour de France - Italian Marco Pantani, who died of a drug overdose in 2004, and German Jan Ullrich.
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