Sharpton presided over the private ceremony held for family and a few friends at the home of Deanna Brown Thomas, Rachel Noerdlinger said.
Also at the service were Brown's partner, Tomi Rae Hynie, and the couple's young son, said her spokesman, Michael Nason said.
The service took place more than two months after the singer died in an Atlanta hospital. Brown died Dec. 25 at age 73, and his body had been held at an undisclosed location since then.
The service was in sharp contrast to elaborate funerals for the Godfather of Soul held in the days after his death in New York and Augusta, Ga., where more than 8,500 people filled an arena bearing his name.
The crypt likely will not be Brown's final resting place. A public mausoleum is being built and its location will be announced once it is completed, Noerdlinger said.
Brown's children decided to use their own money to place his body in the crypt instead of waiting for disputes over his estate to be settled in court, Sharpton said in a statement.
"The children wanted to see their father entombed in a resting place without delay," Sharpton said.
Hynie, who claims she is Brown's fourth wife, and her son were not included in Brown's will. Attorneys for Brown said his marriage to his backup singer was annulled because Hynie was still married to another man.
A longtime friend of Brown and trustee of his estate was disappointed by the service.
The trustees had made arrangements for Brown to be laid to rest at no cost at a "very prominent memorial garden in Augusta," Buddy Dallas told the AP by phone. "Mr. Brown's not deserving of anyone's backyard," said Dallas, who was not at Saturday's service.
Brown's family blamed the delay in burying the singer on issues surrounding his estate.