The German offered his resignation in the wake of his side's humiliating 3-1 defeat to Bologna.
Roma president Franco Sensi had hoped that Voller would reconsider his decision after a meeting on Sunday, but the former Germany coach has decided to leave The Giallorossi.
Voller revealed he took the decision to quit the Italian giants after just 26 days in charge because he could control the side the way he wanted.
"I want to thank President Franco Sensi for accepting my decision to resign," said Voller.
"I am accustomed to dealing with a team in a certain manner," he explained. "I tried to continue doing it my way, but last night I understood that it wasn't the right way for Roma. If I can't control something, then there is nothing I can do to change it.
"The club was behind me 100 per cent and the squad, led by Francesco Totti, asked me to stay on. I feel it is the right thing to do, as I don't think I can help this team. The best way to help them is to put more responsibility upon their shoulders for what is happening here, although in the last few games perhaps I made mistakes too."
Ezio Sella is set to take charge of the side on a temporary basis for next week's Uefa Champions League clash with Real Madrid.
The news of Voller's departure is the latest incident to hit the troubled capital club with Cesare Prandelli resigning before the start of the season due to personal problems.
Roma will now begin their search for a new manager as they look to get their season back on track.
2 gone and its bearly bein 6 weeks of the season
mourinho next ?
