Chelsea won the FA Women’s Continental League Cup for the first time, in front of a competition record attendance of 6,743 at The City Ground.
Bethany England opened the scoring with a close-range finish on the turn in the first half when Arsenal failed to clear the ball.
Ann-Katrin Berger was kept busy in maintaining that early advantage though, denying Louise Quinn and Jordan Nobbs.
The Chelsea goalkeeper also thwarted the efforts of Vivianne Miedema but one such save came at the expense of a corner on 85 minutes, from which Leah Williamson levelled for the five-time winners.
With extra-time now looming, England struck again on 91 minutes when stretching to connect with a Sam Kerr cross at the far post, as the Blues beat Arsenal for the third time this season.
Blues boss Emma Hayes told chelseafc.com: ‘The better team did not win the game; the most resilient team won the game.
“I value defending and I value resilience. It isn’t always about being the best team, it isn’t always about possessing the ball the most.
“This is the third time we’ve played Arsenal this season and the previous two we were extremely dominant in. No-one in our camp thought this would be a dominant Chelsea performance – far from it. To win the game after they out-possessed us, they dominated, shows what a great team we really are.”