The winning ticket was the only nationwide to match all six numbers for the $543 million prize.
The businesses, Lanzilli's Grocery in Eastie and Lee's Supermaket in Brighton, sold Mega Millions tickets worth a combined $4 million in winnings, the Massachusetts Lottery said in a statement.
The prize amount had surged by $10 million from $512m to $522m within a few hours on Tuesday.
KTVU was at the store on South White Road the night the jackpot victor was announced. Winners in Illinois, Kansas and Maryland split $656 million.