One day after the men's team had lost to Liverpool in the showpiece event, Emma Hayes's side made it back-to-back FA Cups after edging a five-goal thriller to complete a league and cup double.
Chelsea's Samantha Kerr had the ball in the back of the net early doors before being pulled back for offside, but there was to be no denying her the opener in the 33rd minute.
At first glance, Millie Bright's cross appeared to evade everyone and nestle into the net, but Kerr got a deft flick on the ball to put the WSL champions in the ascendancy.
Gareth Taylor's side were level on the stroke of half time, though, as Lauren Hemp cut inside before firing home a sweetly-struck effort into the side of the net.
Erin Cuthbert sparked wild celebrations in the 63rd minute as her long-range effort cannoned off the crossbar and into the back of the net, but City substitute Hayley Raso poked home in the 89th minute to force extra time.
Hayes's side were under the cosh during the 30-minute period and faced 23 shots throughout the entire contest, but Kerr made it a brace for herself in the 99th minute after charging into the box and seeing her effort deflect off Alex Greenwood into the net.
City could not find an equaliser as Chelsea claimed their fourth Women's FA Cup title to add to the WSL crown they clinched only a week ago.