After a dominant Arsenal display the Gunners' hard work was undone in the 92nd minute as Beth England clinched Chelsea's first Continental Cup title.
Story of the Match
Despite their dominance Arsenal never took the lead, it was Chelsea who opened the scoring after less than 10 minutes for Chelsea through the in-form England.
Jonna Andersson whipped the ball into the far post, Guro Reiten headed back across and after a loud shout to deter Sam Kerr, England smashed home.
Arsenal were nearly back in it just minutes later after Louise Quinn made a sweet headed effort, only to be denied by a world-class save from Ann-Katrin Berger in the Chelsea net.
The game settled after the opening goal, with the Gunners enjoying a big spell of possession. They had efforts from Jordan Nobbs and Vivianne Miedema saved by Berger.
As soon as Chelsea scored, there was a fear that history was about to repeat itself after the Blues battered Arsenal 4-1 a month ago. A different formation allowed Arsenal to restrict Emma Hayes' side from administering the same kind of beating.
Arsenal weathered the storm and grew well into the game and dominated the remainder of the first-half. Chelsea's chances were scarce but they continued to look threatening on the break.
Most of Arsenal's good play came down the right flank through Caitlin Foord. The Australian, who made her third Arsenal appearance in the final, looks to be as good as people were saying before her January move to North London.
The second half started in the same manner the first ended, Arsenal on top with Chelsea happy to sit back and defend. The counter-attacking capabilities of the Chelsea side were enough to scare Arsenal into not committing everyone forward, to begin with at least.
Arsenal dominated the second half, they had chance after chance and looked by far the better side.
They finally got the goal they deserved with less than 10 minutes to go. Leah Williamson slammed the ball home from close range to get the Gunners back in it.
The Gunners pushed on for the winner with Foord and Miedema both having chances with Chelsea stayed resolute at the back for as long as they could.
Nobbs swung a fierce ball in that was plucked out of the air by Berger. Both sides cancelled each other out. Both seeking that all-important winner.
Chelsea got it through Beth England, securing the first piece of silverware of the season for Emma Hayes' seemingly unbeatable side.
They remain undefeated in all competitions this season and now have beaten Arsenal three times along the way.
Chelsea have now full established themselves as the premier team in England this season, becoming the first team not called Arsenal or Manchester City to win the Continental Cup.
Emma Hayes' side showed grit and determination to not only keep the scoreline at 1-0 for as long as they did but then even more so to nick the winner at the death.
This could be the start of a fantastic treble for the east-London side. They still have the chance to finish the season undefeated in all competitions should they win the FA Cup and league titles.
Arsenal fall to Chelsea once again, having lost 4-1 at Borehamwood earlier in the season. Emma Hayes has Joe Montemurro's number and that's probably down to the fact his tactics are very predictable.
The Gunners still have the Champions League and FA Cup to compete for but are now also outsiders for the league title too. They face PSG in the next round in Europe, which will not be an easy ask for the red and white of North London.