But Ghulam Isaczai's name was removed from the list of speakers early Monday in a move that diplomats suggested had been brokered by Washington, Beijing and Moscow after they did the same for Myanmar.
"I imagine" that there was an agreement struck by those three powers, an ambassador with a Security Council country told AFP.
Another diplomat, speaking on condition of anonymity, described it as a "wise decision."
Last week, the Taliban wrote a letter to UN Secretary-General Antonio Guterres requesting that its new foreign minister Amir Khan Muttaqi be allowed to participate instead of Isaczai.
The group said that Isaczai, who had urged nations to "unequivocally state" that they would not recognise a Taliban government, "no longer represents" Afghanistan at the global body.
But diplomats at the UN said the request had come too late and Isaczai, still considered the head of Afghanistan's mission by the UN, appeared on a list of speakers sent out late Sunday.
"The country withdraws its participation in the general debate," Monica Grayley, a spokeswoman for the assembly's president, told AFP, adding that the mission had not cited a reason for pulling out.
The withdrawal came after a high-level UN diplomat told AFP that an agreement had also been reached between the United States, Russia and China preventing Myanmar's UN ambassador -- an outspoken supporter of the democracy movement -- from speaking.
Kyaw Moe Tun, chosen by former leader Aung San Suu Kyi, has defied the military junta running the country to stay in his post.
He is supported by the international community and has retained his seat at the United Nations following the 1 February military coup.
In May, the junta appointed a former general to replace him, but the United Nations has not yet approved the appointment.
Kyaw Moe Tun was the victim of a recent alleged conspiracy foiled by US investigators that plotted to either force him to resign or kill him if he refused.
He told AFP his plans for the General Assembly were "low profile."
The assembly is expected to be asked to vote in November on which of the competing delegations represent Afghanistan and Myanmar at the UN.
Guinea's representative Aly Diane, appointed by former president Alpha Conde, who was deposed in a military coup earlier this month, said the new military authorities plan to form a "government of national unity" and draft a new constitution before holding "free and fair elections."
"Arrangements have been made to allow political parties and civil society to operate freely," he said, noting that Conde's opponents have also been released.
It was another of several anomalies at the diplomatic marathon, which saw 100 leaders and dozens of ministers descend on the UN headquarters after last year's event was mostly virtual.
Many leaders chose to send video messages instead.
French president Emmanuel Macron initially said he would attend, before opting to send a video message that was to be played the day after US President Joe Biden spoke.
Eventually, foreign minister Jean-Yves Le Drian instead spoke for France, whose presence all week was overshadowed by a spat with the United States over a mega submarine deal with Australia.
Despite being at the UN for five days last week, Le Drian gave his address in a pre-recorded video message Monday that called for Western powers to revive the stalled Iranian nuclear deal.
"It is rare for one of the five permanent members of the Security Council to intervene on the last day," said a European diplomat, on condition of anonymity.
The United States, fearing the event would be a hotbed for the coronavirus, had tried to dissuade leaders from traveling to New York, where a vaccine mandate is in place.
Strict rules over masks and social distancing were imposed, with only seven people per delegation allowed.
Only four positive cases have been reported so far, all in the delegation of Brazil, whose president, Jair Bolsonaro, is a vaccine skeptic.
Despite New York's efforts, delegates did not have to show they were vaccinated or provide proof of a negative test to enter the UN building.
In all, speeches by leaders and representatives from all 193 UN members, apart from Afghanistan and Myanmar, will have been delivered, many focusing on international collaboration on climate change and Covid-19.