Villa were knocked out of the FA Cup by Everton last Sunday and then played out a 1-1 draw with CSKA Moscow in the Uefa Cup on Thursday.
They were below their best in their third game in six days as Nicolas Anelka's excellent goal secured three points for Chelsea.
O'Neill said: "It sounds like an excuse but I do believe the three games in quick succession took their toll.
"At the beginning, we looked leggy and Chelsea got into their stride very quickly.
"We got a bit of momentum before half-time and had a lot of possession in the second half without creating too many chances."
O'Neill admits it has been a difficult week but he is confident Villa can get back on track and hang on to fourth place.
"I am disappointed with the setback but we are far from finished. I suppose it is a sign of how far we have come that we are disappointed at being fourth in the table," he said.
"We have some quality players. You get disappointments but we will bounce back and there is not a dent in our belief.
"I thought we could win today. I still thought that at half-time. In terms of effort and determination they have given everything.
"The top four teams have the squads to cope with hectic schedules and it is something we will have to learn as well. But we are still in there fighting."