More than 300 family members travelled to the region on Friday, exactly four months after the Airbus A320 went down.
The unidentified remains of the 150 victims were buried on Thursday night in a cemetery in the town of Le Vernet, ahead of the memorial service.
Mayor Francois Balique said they had been placed in a mass grave.
"For the families of the victims, it's a second burial because they have already buried the remains of their loved ones that could be identified by DNA," he told AFP.
The aircraft crashed on 24 March during a flight from Barcelona to Duesseldorf, killing everyone on board.
Investigators believe co-pilot Andreas Lubitz deliberately flew the plane into a mountain, after locking the captain out of the cockpit.
There were passengers from 18 countries on the flight, although most were Spanish or German.
All of the remains that could be identified by French police were returned to their families for burial.
The chief executive of the airline Lufthansa, which owns Germanwings, did not attend Friday's interfaith ceremony.
Carsten Spohr has been involved in a disagreement with some of the families over compensation pay outs.
The parents of 16 German students, who were returning from a school trip, said Mr Spohr had failed to apologise for the crash.
In an open letter they said a compensation offer of â‚¬85,000 (Â£60,000; $93,000) "deeply insults us, and above all else our children".
A Lufthansa spokesman said "the tense atmosphere" meant Mr Spohr would not be attending the memorial service, AFP reports.
"He does not want to disturb the ceremony with this issue," a spokesman added.
A ceremony to commemorate the passengers who died in the Germanwings plane crash has been held at the scene of the disaster in the French Alps.