Hayling Island s McIntyre and Mills topped the leaderboard in the fourth race in their class on the waters of Enoshima Yacht Harbour in the early hours.
The Great Britain pairing were first across the line in a time of 38mins 57sec, some 26 seconds quicker than the second placed Swiss duo of Linda Fahrni and Maja Siegenthaler, with Noya Bar Am and Shahar Tibi of Israel in third.
McIntyre and Mills recovered well after coming home way down in seventh in the third race of the Olympic meet earlier in the day.
It followed on from their fourth and third places finishes in the opening two 470 Class races at Tokyo 2020 yesterday.
The GB pairing will be back on the water tomorrow for races number five and six of their class.
McIntyre and Mills are aiming to secure a place on the podium when the women's 470 Class event concludes on Wednesday.