The Pompey boss felt his side were unfortunate to leave London without anything to show for their endeavours after a goal from on-loan Millwall striker Shaun Batt gave the O's a 1-0 victory.
"Without doubt the best team lost for sure," said Whittingham. "Three or four of their players told me that as they were coming off the pitch so I think that tells the whole story, and a mistake by us has cost us the game.
"We knew that we needed high energy, we know that Russell Slade organises his team well. They are good on the attack and have good movement, so we needed that high-energy and we got it all the way.
"I'm just so, so disappointed for all the players because they put so much effort in.
"It was a mistake that led to their goal but these things happen. The players are dejected in our dressing room having come here and done so well and I don't think that anybody could deny that we were the better team. That defeat is hard to take.
"The players are all working hard, they know there's a challenge for Portsmouth and they want to be a part of it and that's fantastic for us."