In front of a home crowd in Birmingham, 27-year-old Yafai won 118-108, 119-107 and 119-107 on the judges' scorecards.
Yafai knocked down the 31-year-old Japanese in the second round, but was caught several times himself on the way to recording his 22nd unbeaten fight.
"I had to box my way through. My hands were in a bad way after two rounds but I did what I had to to win," he said.
"I'm a work in progress, I have to learn how to slow the pace down a bit."
Yafai landed a barrage of punches in the first round, and a slick combination rocked Muranaka in the second, causing him to touch down on to the canvas with a knee.
But Muranaka recovered, walking through Yafai's punches and landing with left and right hooks of his own.
The home fighter took back control in the later rounds and, despite being docked a point for a low blow, Yafai ran out a comfortable winner.
Promoter Eddie Hearn is looking ahead to big things for his fighter after "a great performance".
"One more defence and he has to chase the big unification fights," Hearn said.
Yafai's victory made it a double success for his family, with younger brother Gamal victorious on the undercard.
The younger Yafai was impressive in a seventh-round stoppage of the previously undefeated Sean Davis - a fellow Birmingham super-bantamweight.
The 25-year-old worked the head and body superbly, dropping his opponent six times on his way to claiming the WBC International super-bantamweight title.
Birmingham's Sam Eggington won the European welterweight title with an emphatic ninth-round win over Spain's Ceferino Rodriguez.
Britain's Kal Yafai retained his WBA super-flyweight title with a points win over a game Suguru Muranaka.