Alexandre Lacazette and Pierre-Emerick Aubameyang have been forced to compete with each other for playing time in recent weeks.
The 27-year-old had scored in his previous two matches, but was unable to keep the run going as he missed two major chances before being substituted in the 56th minute.
But Aubameyang’s introduction did not have the impact Emery had hoped, with the Gabon international missing a late penalty which could have given the Gunners victory at Wembley.
Emery was asked about Lacazette’s unhappy reaction to being taken off and fired a warning to both of his forwards, Metro reports.
The manager said: “They need to accept the decision. I am finding the best decisions for the team and they are playing other matches.
“Sometimes I am not happy with them both when their performances are not good when they’re both playing, but I am very consistent in our work to take the best decision and to give them the best performance for us, whether they’re playing together or alone.
“For example, next match it is not possible to play both because of the red card in Europe for Lacazette. I can only play Aubameyang.”
Arsenal face another busy week, travelling to France on Thursday to play Rennes in the Europa League, before facing Manchester United in the Premier League at the Emirates Stadium on Sunday.
Team-mate Granit Xhaka praised Aubameyang for having big “cojones” — and insists they have still got their sights set on top four.
Striker Aubameyang was distraught and inconsolable after seeing his last-gasp penalty as Arsenal missed the chance close the gap on arch-rivals Tottenham to one point with nine games to go.
But Xhaka insists the Gunners have shown enough improvement in recent games to force their way back into the Champions League next season, something he says is vital.
Midfielder Xhaka said: “If you take a penalty in the derby, you have cojones — big balls. Not all of the players would have taken this one. So we are happy he took the penalty.
“If he scores, he scores. If he doesn’t score, he doesn’t score. This is football.”