The Blues visited the London Stadium only four days after securing a 1-1 draw against Atletico Madrid in the Champions League to book a place in the last 16 as runners-up behind AS Roma. It was Marko Arnautovic's early goal which led David Moyes's men to victory.
Moses was introduced into the game in the 55th minute but he was unable to undo what had already been done to the Blues by the desperate West Ham team.
Conte explained the reasons behind the loss, saying, "We lost the game against West Ham; we started badly and conceded this goal, and it was hard to come back".
"Our priority is to play the league", Conte said.
"Today our ideas were not so clear and in the final pass we made a lot of mistakes". Our passing was off, and we didn't create as much as we have been. "When you shoot 19 times in a game it means you attacked, but we can do better".More news: Comedian Hannibal Buress arrested for disorderly intoxication in Miami
However, the Chelsea boss said that he was happy with Bakayoko's display, pointing out that his withdrawal was merely a tactical decision.
The gap between City and Chelsea now stands at 14 points, but Conte insisted that the level of competition for a top-four finish means his players can not afford to take their eye off their domestic commitments regardless of how Monday's draw for the Champions League round of 16 pans out.
Saturday's defeat is the fourth of the season in the league for Chelsea and the chances of them retaining the title they won past year is shrinking with each passing week. "When you have this task, it is impossible to think that you are in the title race", Conte told press after the defeat.
Burnley are level on points with the two north London heavyweights after Scott Arfield scored in a 1-0 home win over Watford, who had Marvin Zeegelaar sent off for a studs-up foul on Steven Defour.