Harrow struck first through Sam Winters but Millfield hit back to lead 14-7 with two superb solo scores through Ben Morrow and Will Stebbings.
Patrick Keaveney cut the gap to two for Harrow, but narrowly missed the kick that followed leaving Millfield with a slender advantage at the break.
George Bullivant showed his pace and power with a superb double to take Millfield into an unassailable lead, with Harrow's final score proving a consolation as Millfield booted the ball into touch from the resulting restart to win a first title since 2014.
It was a stunning turnaround for the tournament's most successful team, and director of rugby John Mallet was full of praise for the resilience his side had shown after a day one defeat to Hampton.
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