Bolton substitute Tamir Cohen headed the winner, leaving Arsenal nine points behind leaders Manchester United with four games left and almost certainly ending their bid to claim a first trophy since 2005.
Arsenal went into the match on an unbeaten 16-game run but a succession of draws had allowed United, who beat Everton 1-0 on Saturday, to open a gap at the top of the table.
"It is difficult to swallow the way we lost," Arsenal manager Arsene Wenger told Sky Sports.
"We had chances to win it but didn't take it and in the end we were caught in the way we feared today, from a corner. The week we have just had summed up our season - lots of quality in our game on Sunday, Wednesday and today but not enough rewards for our effort. We could have had nine points but we got two."
Lee Chung-yong missed two good chances before they took a deserved lead in the 38th minute. Gary Cahill's header from a corner was blocked on the line by Samir Nasri but Daniel Sturridge nodded in the rebound for his seventh goal in nine games since arriving on loan from Chelsea in January.
"After last week, we wanted to show the fans we had the passion to prove to them that was just one bad day," Sturridge told Sky Sports.
"I have done my team Chelsea a favour today but I came out here to work for Bolton and their fans."
Bolton manager Owen Coyle said: "I think everyone knows how bad we felt after the FA Cup semi-final and it was important we showed our character today - and we did that.
"We dealt Arsenal's title hopes a big blow but more important for us was
