German Chancellor Angela Merkel joined crowds for the ceremony at the Kaiser Wilhelm Memorial Church, close to where the vehicle ploughed into festive stalls in the city centre on Monday evening.
Mrs Merkel, German President Joachim Gauck and other senior officials also laid white roses among candles at a makeshift shrine remembering the dead and injured.
Speaking during a televised address earlier on Tuesday, she said: "Twelve people who were still among us yesterday, who were looking forward to Christmas, who had plans for the holidays, aren't among us anymore."
Islamic State claimed responsibility for the attack, which also left 50 people injured, while German police are continuing to hunt for the suspect.
The Anglican Bishop of Europe Rt Rev Dr Robert Innes urged people to pray that Angela Merkel would be able to respond wisely to the incident.
Speaking with Premier, he said: "We should pray for the victims, for their families, for the medical services and their care, and for all who witnesses that traumatic incident as well who will be deeply shocked.
"I think [we should pray] also for the German government, for Angela Merkel and for a wise and proportionate response."
A 23 year old asylum seeker from Pakistan arrested after the attack was released on Tuesday because of a lack of evidence.
Germany's most senior prosecutor, Peter Frank, said the attack echoed July's deadly truck crash in Nice but added: "We don't know for sure whether it was one or several perpetrators.
"We don't know for sure whether he, or they, had support."
Speaking about the best way to respond, Bishop Robert said: We move from fear to faith.
"It's often been said recently, the Bible says 'do not fear' 365 times - one for each day of the year.
"Faith is the opposite. It's that trust in God which we are encouraged to live out, believe in and to practise - that's the world in which we endeavour to inhabit."