Rubio, who joined the Indian side in the beginning of the ongoing season had penned a short-term contract with the club until November 30, 2016.
Bengaluru FC's Spanish manager Alberto Roca had brought in his compatriot mainly for the club's AFC Cup matches.
The official statement from the club read: "Spanish midfielder Alvaro Rubio has called time on his short but impactful Bengaluru FC sojourn after seeing out his contract that ended on November 30.
"Brought in by coach Albert Roca in July to add experience to Bengaluru's AFC Cup campaign, 37-year-old Alvaro was a vital factor in the Blues reaching the final in Doha."
After seeing his contract with BFC, Alvaro Rubio spoke to the club's official website and said: "I had a stupendous experience at BFC.
"Personally, it was a positive development for me and I am very grateful to the players, management, fans and everyone associated with the club.
"I wasn't from the country but they always made me feel home. I am sure that this club has a great future ahead. I would like to thank everyone again and I hope we meet soon."
On Rubio's departure, coach Roca said: "Alvaro was brought with a specific plan in mind for the AFC Cup and he leaves having done everything that was asked of him.
"He's been a great professional and in a short time has managed to be an influence on the youngsters in the team who I believe, have learned much from him. We wish him luck and thank him for his time with Bengaluru FC."
Alvaro Rubio, who has experience of playing over 300 La Liga games for multiple Spanish clubs, brought in a much-needed stability in the side's central midfield.
The 37-year-old showered all his experiences in the 5 matches he played for the club in the AFC Cup. Bengaluru FC missed out on the coveted title after losing to Iraq's Airforce club in the final at Doha.