They are devotees of the French-based Thich Nhat Hanh, a Zen monk who was a confidant of slain US civil rights leader Martin Luther King.
"The last of about 200 followers of Thich Nhat Hanh left our pagoda on Tuesday evening," said Thich Thai Thuan, who heads the Phuoc Hue pagoda in Lam Dong province.
Religious activity remains under state control in Vietnam, although the government says it always respects freedom of belief and religion.
Human Rights Watch has said that pressure on Nhat Hanh's followers was "clearly linked to his call for religious reforms".
In early December, Thai Thuan said that after three days of mob pressure he had "no choice" but to sign a written promise that the devotees would leave his temple by December 31.
A crowd of about 100 people had descended on the pagoda demanding that the monks and nuns depart. One nun claimed that police were among the crowd and that some in the crowd had been paid to intimidate the Buddhists.
The monks and nuns began leaving on December 13, returning to their local communities, to their former pagodas and to a temple in central Vietnam's Hue city, Thai Thuan told AFP.
"For the authorities, we are illegal," Trung Hai, a monk representing the group, said last month in Geneva.
Almost two weeks ago a delegation representing Nhat Hanh's followers asked France for temporary asylum, saying the group no longer felt safe in Vietnam.
The abbot at Phuoc Hue said Wednesday that he had no details of the asylum request but he understood about 20 monks had left Vietnam for France and Thailand.