Despite a valiant display from the Red Devils against the defending champions, a host of missed chances cost them, as a second-half Samantha Kerr strike saw the Blues retain their crown and keep hopes of another domestic double alive.
Starting in the mould of a team with ambitions of winning a first-ever piece of major silverware, Man United exploded out of the blocks at Wembley and had the ball in the back of the net within just 20 seconds through Leah Galton.
The Blues failed to clear their lines and Galton fired home from close range, but the lineswoman's flag belatedly went up, with Ella Toone marginally offside in the build-up.
Despite that early reprieve, Chelsea remained on the back foot as Marc Skinner's side continued to foray forward at every opportunity, with Ann-Katrin Berger called into action to thwart Nikita Parris's curler in the 15th minute.
Emma Hayes's number one saved her side's bacon again in the 32nd minute, as a deep Katie Zelem free kick caused chaos in the Chelsea box before falling to Millie Turner, whose close-range deflected effort was brilliantly clawed away by Berger, who was already on her way down before sticking out a strong left hand.
Galton flicked another golden chance over at the near post in the 37th minute, and having absorbed copious amounts of Red Devils' pressure, Chelsea arguably had the best chance of the half four minutes before the break.
A looping header from former Man United attacker Lauren James appeared to be dropping into the back of the net, but a back-pedalling Mary Earps tipped her compatriot's effort onto the post as Man United survived.
Hayes unsurprisingly introduced Pernille Harder early in the second half, and the 30-year-old had her first sight of goal not long after in the 59th minute, but she could not adjust her feet quickly enough from Kerr's pass and shot straight at Earps.
However, Chelsea's deadly duo soon combined again, and this one proved telling. Guro Reiten set Harder away down the right, and the striker picked out Kerr's run to the back post for the Australian to prod home the opening goal before the customary backflip celebration.
For all of Man United's previous threat, one sweeping attack from the Blues did the damage, and Kerr should have turned provider for an insurance goal for her side in the 81st minute - nutmegging Maya Le Tissier on the left and cutting back for an arriving Sophie Ingle, but her effort was high and not very handsome.
In the sixth and final minute of added time, Chelsea's defence survived one final scare, as Berger flapped at a cross and put the ball on a plate for Galton, but the Man United attacker could not fire home through a sea of bodies as the Blues celebrated FA Cup glory for the fifth time.
Attention now turns back to the Women's Super League title fight for both sides, with Man United sitting one point clear of Chelsea at the top of the table, but the FA Cup winners boast a game in hand.
Hayes's side have three days to celebrate before they visit West Ham United on Wednesday, while Skinner's runners-up host local rivals Manchester City next Sunday.