The 109 Vietnamese, many of whom have lived in Europe for several years, left Berlin's Schönefeld airport later Monday, police said.
The group of demonstrators fighting for the asylum-seekers' right to stay had tried to organise a sit-in in the airport's Terminal A, from which the Air Berlin flight was to leave, but were removed by police.
"This is the first time in years that there has been an organised deportation of a group from Berlin, even if there have been some from (the western city of) Frankfurt," said Green city counsellor, Wolfgang Lenk, who turned out to support the protest.
"It is obvious that group deportations usually prohibit the individual files from being studied closely."
He added that activists were concerned that some of those sent back to Vietnam could face reprisals.
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"We are protesting primarily against the fact that we are deporting people to a country like Vietnam that violates human rights," he said.
Two people, aged 18 and 24, were briefly detained but released after the protesters dispersed, a police spokesman said.