"I am tendering the resignation on the basis of the election results," Gilani told a news conference in his hometown of Multan.
"The PPP did not want to contest the May 11 elections but President Asif Ali Zardari did not let us do so," he said.
However, he did not agree that voters "punished" the PPP for failing to tackle issues like power cuts and inflation.
"Time will tell about our government's services for the country," he said.
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The PPP wanted to convene a public meeting in Multan on May 9 but could not do so due to security concerns while his son, Ali Haider, was abducted two days before the polls, he said.
Sources told PTI that Gilani had resigned from the party post because he wanted to maintain a low profile.
"Gilani's son, Ali Haider, has been kidnapped and there is a threat to the other members of the Gilani family," a source said.
Police are yet to make a breakthrough in tracing Gilani's son or his abductors.
Gilani said his disqualification had been a "big blow" for the PPP.
He said he had no differences with the PPP's leadership but called for the party to be reorganised.
A new leadership should take on the responsibility of heading the party, he said.
For now, the PPP had emerged as the second largest political party in the polls and would play the role of an active opposition, he added.