Many of those who attended mosque with the couple refused to attend, two mosque members said.
US-born Farook, 28, and his Pakistani-born wife Malik, 29, killed 14 people and injured 21, in what US officials have called a terrorist attack.
They died later that day in a gun battle with police.
The funeral followed traditional Islamic rituals.
At a Muslim cemetery hours away from San Bernardino, the bodies were cleansed according to Islamic rules, wrapped in white cloth, and buried.
It reportedly took a week to find a graveyard willing to accept the bodies.
Muslims are usually buried within 24 hours of dying, but family members and community members had to wait for the bodies to be released by law enforcement officials and then for permission from a cemetery.
A woman at the Islamic Cemetery and Masjid in Adelanto, less than an hour from San Bernardino, confirmed the cemetery had refused to bury the bodies, in part out of a fear of backlash, but also for “other reasons”.
The family of Tamerlan Tsarnaev, one of the two men accused of carrying out the Boston Marathon bombing attack in 2013, faced similar difficulty finding a place to bury his body after the attack.
The family ultimately buried him in an unmarked grave in Virginia.
About 10 people went to the funeral, an attendee said, including members of Farook’s family and people who used to pray with him at mosques in San Bernardino County.
Most Muslims in the community refused to participate in the burial or perform the funeral prayer, called Salat Al-Janazah, according to the source, who did not attend the funeral.