Emma Hayes’ injury-hit side started the day a point behind United, albeit with a game in hand, but Kerr’s 23rd-minute goal decided a tight game and gave Chelsea a huge win in a thrilling title race.
United dominated possession early on but were given two warnings as Kerr twice tested visiting goalkeeper Mary Earps.
Lauren James played a pinpoint ball over the top from the right touchline, Kerr timed her run to perfection, brought the ball down on her chest, then lifted it gloriously over Earps and into the far corner.
United felt they should have had a penalty in the 33rd minute when Nikita Parris went down under contact from Kadeisha Buchanan, but referee Cheryl Foster waved played on.
Kerr remained Chelsea’s main threat in the second half, muscling Maya le Tissier off the ball before side-footing just wide.
And while United pushed for a leveller in the closing stages, they failed to create any clear chances and the hosts held on.
“We deserved it – that was a Chelsea performance,” Hayes said.”Depleted – we have a sickness bug in the camp – we couldn’t play Erin Cuthbert carrying a knock and Jelena Cankovic is carrying a knock too.
“It’s just a massive three points and when we came into the game, we had played two games more than Manchester United since they last kicked-off.
“They played Leicester earlier last weekend, so to win like that and against a team who are top of the league is amazing for my team – fantastic effort.”
Chelsea are now two points clear at the top as they bid for a sixth WSL title.
In a game of few chances, Kerr was a threat throughout with her very presence seeming to unnerve a United backline that had been breached just eight times in the WSL this campaign.
An early ball over the top was not fully dealt with by the away team and Kerr was able to steal in and bring a save from Earps.
After 12 minutes, Melanie Leupolz slid the ball through to Kerr and after holding off Le Tissier, saw her left-footed shot saved by the legs of Earps.
At the home of the defending champions, they controlled possession for long spells of the game and, for all that Kerr tormented the defence, they still managed to limit Chelsea’s opportunities.
“We knew we are going to be without the ball for large periods and everyone was disciplined in their roles which they carried out the gameplan to perfection, ” Chelsea boss Hayes said.
Toone had the chance to create something just after the goal but she and Alessia Russo were largely kept quiet by Chelsea.
The title race still has a way to go but with Chelsea in a position to stretch their lead to five points by winning their game in hand, there is no more margin for error and United cannot afford another off day from an attack that has been so prolific for much of the season.