Goals to Andrew Johnson and Andranik and a hat-trick to Norwegian striker Erik Nevland did the damage for the London club who impressed Glory boss Dave Mitchell.
"They looked like they put their foot down in the second half and really came at us," Mitchell said. "They're a quality side.
"They just showed us how to close down well as a unit, as a team. They were really well organised and they caused us problems.
"For long periods of the game I was happy. Obviously once they scored one or two goals our heads dropped a bit."
Fulham must now prepare for a Europa League qualifying match in two weeks whilst the Glory will meet North Queensland Fury in Mandurah this Saturday before playing Gold Coast United in Bunbury next week.