The defeat was Barca's second consecutive on the road and dropped the Catalan side to third in the Primera Division standings - four points behind leaders Real Madrid.
The latest setback increased speculation over the future of the 51-year-old Martino, who replaced Tito Vilanova at the helm of the Spanish champions last summer.
"Martino has a contract with us until June 2015," Bartomeu told radio station Cadena Ser. "We would like Martino to remain with us next season.
"We hope he will remain with us for a long time.
"He is eager to do things well and win."
Bartomeu confirmed Barca will bring in at least two new faces this summer, with goalkeeper Victor Valdes and veteran defender Carles Puyol leaving the club at the end of the season.
"We have two definite signings," he said. "One is a goalkeeper and the one is a central defender.
"Over the last year we have looked at a long list of goalkeepers and we have narrowed the selection of those that are more adequate for the position.
"We have spoken to them.
"The fans can be calm regarding this."
Bartomeu is nevertheless hoping that long-standing club captain Puyol will change his mind and stay.
The 35-year-old announced last week his decision to leave Barca this summer after 15 years at the club, but did not reveal his future plans.
"We would like him to continue at the club," Bartomeu said of the former Spain international, who has been plagued by injuries in recent years.
"He is a model player. He symbolises the essence of Barca."