Ellen White scored a late header to earn the victory to and settle a tough contest against a stubborn Japan side.
White has been the star of Team GB so far at the Olympics after scoring a brace in the opening 2-0 win against Chile.
The result sees Hege Riise's progress into the knockout rounds with a game to go in the group stages.
Team GB struggled to find their best form in the first half with Japan creating the better chances without really testing goalkeeper Ellie Roebuck.
The Brits responded well after half-time and Nikita Parris came close with a great effort after 67 minutes but it went just wide.
Team GB took the lead seven minutes later when White got on the end of a Lucy Bronze cross to head the ball home.
It was a fine header from White but the ball looped into an empty net after goalkeeper Ayaka Yamashita mistimed her clearance.
"We're very happy with two wins and that puts us in the position to rest players and recover for the knockout stages," Riise said.
"We were a different team in the second half, we had the togetherness I want to see and we were totally committed."
Team GB held on for the win and will face second-placed Canada in the final Group E game on Tuesday.