Frank Lampard's 200th career goal for the Blues and a second-half strike from the lively Eden Hazard saw the Hammers go down 2-0 in West London.
Allardyce would have liked to have seen his Hammers team sneak a goal but admits Chelsea were too good, with Hazard and Juan Mata causing particular problems in midfield.
"Overall, yes they deserved to win, but I'm a little disappointed that we might have just sneaked one and just seen how they handled it," he told Sky Sports.
"I think, at the end of the day, Chelsea are a top, top side and were in good form today, especially the clever players. We had a lot of trouble trying to cope with them today.
"But it doesn't define our season playing against Chelsea at Stamford Bridge and losing."
The defeat leaves West Ham 14th in the table with 33 points and Allardyce is keen to reach the 39-point mark sooner rather than later to avoid being dragged into the relegation mire.
On their points target this season he added: "I'd say 39, because it's the average over the last 10 years. It probably might be 38, who knows, but all we want to do is get to it as quickly as we can and have a few games left if we can because that would mean that we would finish in a position in the league well clear of the bottom four, and that's what we want to try and do."