The motion was initially voted down, before a subsequently amended attempt was successful.
"Today the State Delegates Council of the NSW Greens abandoned grassroots democracy by overturning a democratic preselection result," Mr Buckingham said.
"They also threw justice under the bus by abandoning their own policies and due process to reward bullying behaviour and the lynch mob. This was a key test of principles for the NSW Greens and it has unfortunately failed that test."
Mr Buckingham's removal from the ticket is unlikely to end the internal instability within the party, but instead is likely to exacerbate the existing factional feuds.
It is understood a substantial part of the delegates' debate centred on how to determine who should replace Mr Buckingham on the ticket - and whether a recount of votes from the party's upper house preselection in May was required.
Adding to the drama, a party source said delegates were told the integrity of the postal votes from the preselection could not be guaranteed due to two break-ins at the Greens head office this year, as well as a relocation of their office.
A total of 2565 NSW Greens members voted in the preselections, from about a 4000-strong membership base. It is not known how many of these were postal votes.
The issue is further complicated by the prospect that Mr Buckingham's removal from the ticket could see the redistrubition of the votes he received in the preselection alter the outcome of who is endorsed in the lucrative second spot.
Mr Buckingham secured the second highest number of votes at the May preselection - behind David Shoebridge, who received 1161 primary votes.
However, he was relegated to the third - and likely unwinable - spot due to the party's affirmative action rules which require at least one of the top two spots be held by a woman.
As a result, Abigail Boyd, who is allied with Mr Shoebridge, secured the second spot.
However, Greens sources said a full recount and redistribution of Mr Buckingham's voted could see Dawn Walker, an ally of Mr Buckingham's, jump into the second position in a move that would all but guarantee her re-election.
Ms Walker gave her valedictory speech to the upper house last month, after she received the fourth and unwinnable spot on the party's ticket.
The internecine war inside the party burst into the public domain last month when Greens MP for Newtown, Jenny Leong, used parliamentary privilege to call on Mr Buckingham to stand aside amid accusations of bad behaviour, which she said did not only include sexual harassment.
Former Greens employee Ella Buckland complained to the Greens in April about an alleged sexual harassment incident involving Mr Buckingham that occurred in 2011.
Mr Buckingham has denied the allegations. An internal investigation by WorkDynamic was launched after Ms Buckland's complaint.
The report found there was insufficient evidence "that a reasonable person could conclude, on the balance of probabilities, that an incident/incidents of sexual harassment as defined by the legislation has occurred".
The issue has spectacularly ruptured the Greens partyroom. Ms Leong's speech in Parliament was supported by fellow MPs David Shoebridge and Jamie Parker, while Justin Field, Dawn Walker and Cate Faehrmann warned it was a "political weapon".
Senator Mehreen Faruqi, a former NSW upper house MP, also issued a statement with Ms Leong, saying Mr Buckingham should stand down.