Their chartered flight landed at 6:40 am, marking the 38th deportation flight from Germany to Afghanistan since December 2016.
A total of 1,035 failed asylum seekers have been sent back to Afghanistan since then.
The deportations have been deeply controversial, with critics saying that the war-torn country is too dangerous to send asylum seekers back to.
Demonstrators had gathered near Berlin airport's Terminal 5 Wednesday evening ahead of the flight's departure, protesting against the asylum seekers being sent back to Afghanistan.
Some of the demonstrators blocked access roads, others forced their way into the premises on the south-eastern edge of Berlin, airport police confirmed.
About 50 to 75 people had been expected at the demonstration, which was approved beforehand by Berlin authorities, but 350 people turned up.
The Brandenburg Refugee Council, which expected a deportation flight to Afghanistan to leave on Wednesday evening, had called for the protests.
Protest went peacefully
Demonstrators chanted slogans and held placards calling for the deportation flight to be cancelled.
Despite a brief scuffle between officers and protesters, the demonstration went off peacefully on the whole, a police spokesman said.
Police asked several demonstrators to leave, but no-one was detained. The protest ended after the plane departed for Afghanistan, the spokesman added.
Almost daily attacks by Taliban militants are taking a toll on Afghan civilians. The Islamic State militia is also active in the country.
Despite the start of peace talks, the conflict between the Taliban and the Afghan government continues.
Afghanistan has been a battleground for four decades. In addition to regular clashes across the country, targeted killings and bomb attacks occur more often around the country, including the capital Kabul.
