Kerr, who has netted six goals in the competition this season, fired in a cross from Pernille Harder and celebrated in front of Chelsea supporters with her trademark backflip.
The game had been finely poised until Kerr broke the deadlock despite Manchester United, competing in their first major cup final, being on top for most of the first half.
Marc Skinner's side, who have never defeated Chelsea, imposed themselves early on when Leah Galton had a goal ruled out within 23 seconds of kick-off for offside.
United had an edge after the chaotic start and came close again when Millie Turner almost stabbed in a loose ball on a free-kick, before Galton sliced Alessia Russo's low cross wide at the near post.
But Chelsea always carried a threat through Lauren James, who looped a header which was expertly tipped on to the post by goalkeeper Mary Earps.
With 77,390 watching on at Wembley - a world record for a women's domestic match - Chelsea began to impose their quality after the break.
Substitute Harder eventually provided the extra quality they needed when she teed up Kerr, ensuring Chelsea became the first side since Arsenal in 2008 to win three Women's FA Cups in a row.
It is their fifth FA Cup crown overall and the latest in a growing list of phenomenal achievements by Emma Hayes' side - and she will hope to add more in a few weeks' time as Chelsea remain locked in a fierce Women's Super League title race with United.
Chelsea's achievement, winning a third consecutive FA Cup crown, will not come as a surprise given their relentless hunger for silverware - but it's still an immense feat.
They have been the team to beat for several seasons under Hayes and each year have faced increasingly ambitious opponents.
United are the latest to develop and will no doubt challenge again but today, Chelsea showed their superiority in the moments when it mattered.
"When I watched the kick-off and we didn't execute it well, or the second or third phase, then they scored, I thought 'this is going to be a long game'," said Hayes.
"It is so difficult to play again and again. We were just off everything in the first half. I said to the girls at half-time that 'this is the grind'.
"We have done it before. Yes, Manchester United had the first half but we had the second half."
Kerr, recently named Football Writer's Player of the Year, has led from the front all season, scoring goals and carrying a weight of responsibility on her shoulders as other senior players struggled through injury.
It was fitting then that it was Kerr who delivered the match-winning strike - again - linking up with attacking partner Harder, who only returned from a long-term injury this month.
Hayes has often described Kerr as the world's best striker and she always turns up on the big stage - netting in six successive cup finals for the Blues, including the extra-time winner over Manchester City in last year's FA Cup.
Knowing Kerr just needs the one chance was in the back of everyone's mind and, when Harder drilled it across the box from the right, the Chelsea supporters behind the goal had already started to celebrate.
Manchester United have still never beaten Chelsea in any competition
United were in unknown territory having reached their first final but they did not show any sign of stage fright.
Having reformed the women's team only five years ago, their astonishing rise to the top of the WSL table and to the FA Cup final was already an achievement in itself.
And this is a squad packed full of winners - including four Lionesses who won Euro 2022 at Wembley a year ago.
They showed their intent in the first half in particular, being the better side for large periods, but as the game wore on, Chelsea began to take control.
United centre-backs Turner and Maya Le Tissier were in fine form, playing out from the back and largely managing Kerr's dangerous runs in behind.
But United's lack of ruthlessness in key moments proved costly.
Turner and Galton's chances in the first half were squandered, Russo's efforts went straight to goalkeeper Ann-Katrin Berger and a late scramble in stoppage time was cleared by Chelsea.
It was a harsh lesson in fine margins but United showed they belong on this stage and they will be back again. They still have a WSL title to compete for and now they have experienced the Wembley arena, they will surely be hungry to return.
"We started well and, considering Chelsea had been in many finals, we looked like the team that had been in many finals too," said Skinner.
"It's a different type of game in a final and you have to play with more maturity. I thought we played with maturity. We want to be where they were today - so that's what we'll strive for."