According to a statement from Academy of Motion Picture Arts and Sciences President Tom Sherak, Murphy didn't want to continue with the gig after the loss of Ratner.
"I appreciate how Eddie feels about losing his creative partner, Brett Ratner, and we all wish him well," Sherak said.
The "Tower Heist" star didn't specifically address his reasons for resigning, but said he is sorry things didn't work out for everyone involved.
"First and foremost I want to say that I completely understand and support each party's decision with regard to a change of producers for this year's Academy Awards ceremony," Murphy said in the statement. "I was truly looking forward to being a part of the show that our production team and writers were just starting to develop, but I'm sure that the new production team and host will do an equally great job."
Ratner submitted his resignation to the Academy on Tuesday after making headlines with his recent comments about a sexual relationship with actress Olivia Munn and, at a screening of "Heist," using a gay slur, claiming, "Rehearsal is for f--s."
"Over the last few days, I've gotten a well-deserved earful from many of the people I admire most in this industry expressing their outrage and disappointment over the hurtful and stupid things I said in a number of recent media appearances," he wrote in a letter to the entertainment industry. "To them, and to everyone I've hurt and offended, I'd like to apologize publicly and unreservedly."
No word yet on who is in talks to replace Ratner or Murphy. The 84th annual Academy Awards will be broadcast live on February 26.