In a statement, the team said that the relationship ended "by common consent". The announcement means this weekend's race in Abu Dhabi will also formally bring to a close Alonso's five-year spell with the Scuderia, which has yielded 11 wins and 44 podiums, though no championship success.
"Today is not an easy one for me, because even if I always look to the future with great enthusiasm and determination, at the end of this season my journey as a Ferrari driver will come to an end," Alonso said.
"It was a difficult decision to take, but a carefully considered one and from start to finish, my love for Ferrari was a prime consideration. I have always been lucky enough to make my own decisions about my future and I have that possibility now too. I must thank the team for that, as it understood my position.
"I leave Scuderia Ferrari after five years, during which I reached my very best level professionally, tackling major challenges that pushed me to find new limits. I also proved to be a true team-player, putting the interests of the Scuderia before my own. When I had to take important decisions about my future, I did so with Ferrari in my heart, driven by my love for the team.
"I am very proud of what we have achieved together. Thanks to the efforts of the men and women of Maranello, on three occasions we came second in the Formula One world championship, two of them fighting for the title right up to and including the final race, running in a championship winning position for many laps. Without a shadow of a doubt, these five years produced some of the best moments of my career and I also feel that, in leaving the team, it is family rather than friends I am leaving behind.
"Now I look to the future with great enthusiasm, knowing that part of my heart will always belong to the Prancing Horse. I want to thank each and everyone of the team for the trust they showed in me."
Ferrari team principal Marco Mattiacci added: "In the Scuderia Ferrari roll of honour of great drivers, Fernando Alonso will always occupy a special place. We offer him our heartfelt thanks for what has been an extraordinary adventure with the Scuderia, when in the past five years, he twice came so close to winning the world championship.
"I am sure that a great driver like Fernando will always hold the Prancing Horse dear to his heart and I also expect the Ferrari fans will continue to hold him in high regard in his future endeavours."
Alonso has been heavily linked with a move to McLaren, who will switch from Mercedes to Honda power for the 2015 season. The team said recently that they will not announce their driver line-up for next year before December.