Chelsea were second best for most of the afternoon against Manchester United but Kerr scored the only goal midway through the second half to ensure they came out on top.
Victory gives Chelsea their 13th major trophy under manager Emma Hayes and denies United their first ever piece of major silverware.
There was a crowd of 77,390 at Wembley, a world record for a women’s domestic game, and they witnessed a dramatic start when United had the ball in the net after 20 seconds.
United celebrations were short-lived as Ella Toone was just offside in the build-up but they were the better team in the first half, shackled Kerr well and had good chances through Millie Turner and Leah Galton.
Chelsea struggled to get going in the first half but they did go close when a looping header from Lauren James was brilliantly tipped onto the post by United goalkeeper Mary Earps.
United continued to enjoy the better of it at the start of the second half but the introduction off the bench of Pernille Harder transformed the game for Chelsea.
Harder had a massive impact and she set up the winner when she sprung the offside trap down the right and crossed for Kerr to bury a finish at the back post.
It was the third successive FA Cup final that Kerr had scored - and she celebrated with a back-flip.