The 61-year-old Spaniard lasted just six months on his return to Merseyside, with Everton dropping down to 16th position on the Premier League table, six points above the relegation zone.
Everton are on a woeful run of form in the Premier League, having won just once in the top flight since September.
"We knew it wouldn't be easy, and that it was a big challenge, both emotionally and in terms of sport," Benitez said in a statement posted on his official website.
"My love for this city, for Merseyside and its people, made me accept this challenge, but it is only when you are inside that you realise the magnitude of the task.
"From the very first day, my staff and myself worked as we always do, with commitment and full dedication, we didn't only have to get results, but we also had to win over people's hearts.
"However, the financial situation and then the injuries that followed made things even harder. I am convinced that we would have been better once the injured players were back and with the arrival of the new signings.
"The road to success isn't easy and sadly, nowadays in football there is a search for immediate results and there is always less and less patience; unfortunately, circumstances have determined the results and it won't be possible to continue this project."
