"In respect to the decision of the Parliament, the last two times they gave me a vote of confidence, but this time they did not and I accept that," Wardak, who had held the job for 10 years, said in his resignation statement issued to reporters Tuesday.
"This is my final meeting with you to say farewell, and I appreciate and honor the hard work of the Afghan army's soldiers and officers that have sacrificed themselves for the defense of this country."
The New York Times reported Wardak had helped build the Afghan army.
On Saturday, Parliament voted to dismiss him and Interior Minister Bismillah Khan Mohammedi, top ministers in the Cabinet of Afghan President Hamid Karzai.
The Times reported Afghan lawmakers had complained of troubles in the Defense Ministry, including its contracting procedures and failure to respond to cross-border attacks. But some in the government also said several Parliament members were not happy their recommendations for appointments had not gone through.
Karzai had asked both Wardak and Mohammedi to stay on until their replacements had been found.
The latest developments come as the United States and NATO prepare to end their combat operations in Afghanistan by 2014.
In his statement, Wardak said when he took over as defense minister there were barely 50,000 Afghan National Army troops but "now we have 195,000 soldiers in the Ministry of Defense, and I am proud of every moment's activities of the ANA troops in this country."