In the face of the club's off-field woes, the players put together 14 wins to book a place in the top eight.
They will now be demoted to ninth place on the ladder after being forced to forfeit their place in the finals as part of the sanctions handed down by the AFL Commission.
Little admits the players will feel "let down" by the club after toiling so hard all year.
"I think the players clearly have felt the strain over the last five or six weeks and there was a lot of pressure on them," he said on Tuesday night.
"It had been building. I think what I can say to the players now is that there is a clear way forward, and ask them to forgive us for the mistakes we've made."
"I think the players probably do feel let down."
Little confirmed the health of the playing group was being monitored as a result of the experimental supplements program.
With finals out of the question, the Bombers must find one last effort when they take on Richmond in a dead rubber on Saturday night.
"This will be an incredibly tough time for all Essendon supporters and Essendon members," Little said.
"I share their pain. We are terribly sorry for what's happened. I firmly believe now that what we've done today will put this matter to bed and hopefully we can move on from it.
"I don't think there's any doubt there will be some very sad, very disappointed and maybe even disenfranchised people out of the Essendon family. However we must rebuild and we will rebuild."
"I think you'll find that Saturday night that Essendon players will be playing for James Hird and the club."
