Until his 97th minute effort Josh Maja's second-half penalty had looked likely to give the Cottagers a hugely valuable three points in their battle against relegation.
Arteta said "We started really well, controlling the game and creating chances, scoring a goal that was disallowed, in a very disappointed way, we kept going and didn't allow any shots on target and suddenly we concede a penalty and the game changes completely.
"We took risks in the right way, we could have scored three or four, we totally deserved to win the match but put ourselves in a difficult position.
"We have to just focus on the boys playing away in Europe and arriving here with the desire to go all the way to the 97th, 98th minute."
On Alexandre Lacazette's injury, the manager explained: "He felt his hamstring so we don't know. We have to rotate players, we have players who didn't recover from the game on Thursday. That is the risk. You cannot change those players every game.
"We had 16 shots, probably not enough on target, goals disallowed, a post, that is the difference, you have to win this game."