The Blues led early on through Sam Kerr’s superb header from a corner, but Brighton levelled in copycat style thanks to Aileen Whelan’s header.
A much-changed Chelsea, who left key strikers Pernille Harder and Fran Kirby on the bench, dominated but created little against a well-drilled defence.
And Megan Connolly’s corner eluded everyone to earn the visitors victory.
Connolly’s left-wing set-piece at a snowy and windy Kingsmeadow ensured just a third win in 14 league games this season for Brighton, who move up to eighth in the table.
Chelsea remain top but missed a wonderful opportunity to further extend their lead following Manchester United’s surprise home loss against Reading.
A home victory, a 19th successive win in all competitions, looked likely following Kerr’s goal from Erin Cuthbert’s set-piece – the Australian’s 10th in 13 games this season.
But a side who had lost eight of their 14 league games this term replied through a similarly imposing header from Whelan – just Brighton’s 10th goal this season.
Brighton sat deep but pressed aggressively as soon as the Blues crossed the halfway line – a tactic that disrupted the home side’s fluency.
Beth England had a shot deflected onto the bar, but the hosts lacked tempo and quality and were restricted to a series of wayward long-range strikes.
A frustrated and vocal Blues boss Emma Hayes made a triple change just over 10 minutes into the second half, Jo So-Yun adding much-needed creativity in midfield and Kirby and Harder – with 19 goals between them – injecting greater pace and movement.
But despite strong, persistent pressure chances remained at a premium, and Connolly snatched an improbable win on a rare Brighton attack when stand-in keeper Carly Telford made a mess of a near-post corner with 12 minutes left.
Chelsea manager Emma Hayes:
“Our intensity and our aggression was really poor today. You have to take the game to the opponent and you have to work for spaces and chances and I don’t think we did that well at all.
“We’ve given away two set-piece goals which I don’t think we’ve done in my whole time here. They had three shots on target and scored two goals. That’s extremely poor from us.”
Brighton boss Hope Powell:
“It was a demanding, tough game. We had to be disciplined with hard work and good effort and if you do those things you give yourself a chance of winning the game.
“I’ll take some luck against a side like Chelsea – you take all the luck you can get.”
