The Toffees were without 11 players for the Europa League game in the Estadio da Luz, and their inexperience showed as a rampant Benfica put their defence to the sword.
But Moyes refused to criticise his team after the heavy loss, saying it was difficult for players who were playing out of position.
"It wasn't a second string defence, it was playing out of their position," he said.
"We put out the best we had and the players did as well as they could. I only have praise for the players tonight.
"I have said to the players that this is a different competition and we have had two wins and a defeat so it's not that bad.
"Obviously tonight's defeat was not what we wanted but I would like to play Benfica with my best side."
ThreatThe Portuguese team looked dangerous every time they came forward in attack, and full backs Dan Gosling and debutant Seamus Coleman were exposed on a number of occasions.
"Benfica were very good and capitalized on some mistakes we made, and took their opportunities very well," Moyes added.
"I think they had a good attitude and for me they showed their attacking qualities, especially in the second half.
"I thought (Angel) Di Maria tonight was a throw-back winger and he seemed a very good find.
"It shows them (the youngsters) the level they have to play at to get to the top."