The decision was made after a three-hour meeting which started at 2.30pm at the party headquarters in Tropicana, Kuala Lumpur.
At a press conference following the supreme council meeting, party secretary-general Saifuddin Nasution said that the decision to sack Zulkifli was unanimous.
By sacking Zulkifli, the party has opted to cut off the wound which has been left festering for over a year.
In so doing, PKR lost another MP following the defections of Bayan Baru MP Zahrain Hashim, Tan Tee Beng (Nibong Tebal) and Mohsin Samsuri (Bagan Serai), resulting in PKR trailing behind opposition ally DAP with 27 MPs in Parliament.
All three have declared themselves Independent, and Zulkifli (left) is also expected to join their ranks in Parliament.
The supreme council has requested Zulkifli to vacate his parliamentary seat "with immediate effect" but he is unlikely to do so.
However, Saifuddin said he is allowed to appeal the decision within 14 days.
Asked if he does not want to vacate the seat, Saifuddin stressed that PKR members subscribe to an oath to serve the people.
"We feel he has violated the oath with his actions," he said.
Questioned if Zulkifli wants to be an independent MP, the party secretary-general said it would be up to him.
"He is elected under the PKR ticket and he should resign."
Yesterday, Saifuddin said the party disciplinary board, which was tasked to probe two charges against the errant party leader, had completed its investigation.
According to the party constitution, Zulkifli could be given a stern warning, suspended or sacked from the party.
The disciplinary board probed Zulkifli over a police report he had lodged against PAS Shah Alam MP Khalid Samad and for his scathing criticism of Penang Chief Minister Lim Guan Eng.
The Kulim Baru MP had however claimed that he was brought before the board for his opposition to the party's stance on the 'Allah' issue.
Zulkifli, an ordinary PKR member, had walked out of the disciplinary board in protest against the presence of non-Muslim members on the panel.
It is learnt that the board recommended that Zulkifli be kicked out from the party.