The Hammers were thrashed 5-0 by their London neighbours.
Moyes said: "Probably the [comeback 2-1 win in the] Tottenham game played a big part in today. Mentally and physically we found it tough.
"We got a good win at Tottenham. If you had given me two draws in the two away games at Tottenham and Fulham I would probably have taken it, so to get three points is not bad.
"Today I think we were below it physically. It was just what we had.
"Nevertheless, Fulham played well. It went from bad to worse. We'll pick ourselves up and go again on Thursday."
On recovering in time for Thursday's final Europa League group game against Freiburg, Moyes added: "Let's see how the players come back.
"We'll give them a chance to recover, recharge their batteries and hopefully it will be a much better performance than we have seen today."