Mayra Ramirez and Guro Reiten netted second-half goals for Chelsea as they collected a seventh straight league win.
Still without star Australian striker Sam Kerr, they moved to 21 points, two ahead of second-placed City, with a game in hand.
Australian coach Dario Vidosic's Brighton & Hove Albion are three points further back in third after keeping pressure on with a 3-2 win over West Ham thanks to Fran Kirby's 82nd-minute goal.
There was plenty of bite to the top-of-the-ladder clash as Chelsea seemed content to allow their visitors to have the majority of the possession, but both sides cancelled each other out as they struggled to get shots on target.
Ramirez finally broke the deadlock in the 75th minute, appearing to nudge City defender Kennedy to get on to Maika Hamano's pass before running at goal, cutting inside Alex Greenwood and slotting the ball past Ayaka Yamashita.
Blues winger Guro Reiten sealed the win four minutes later as City failed to clear her corner and the ball made its way back to her on the right side of the penalty area, and the Norwegian curled it beautifully inside the far post to make it 2-0.
Fowler was subbed off in the 80th minute for Chloe Kelly.
Earlier in the afternoon, Arsenal continued their recent resurgence with a resounding 3-0 win over Tottenham Hotspur to move up to fourth in the table.
There were five Matildas involved in the north London derby, Caitlin Foord, Steph Catley and substtiute Kyra Cooney-Cross for the Gunners and Clare Hunt and Hayley Raso for Spurs.
Foord was subbed off in the 64th minute for Beth Mead, with Alessia Russo (2nd minute), Frida Maanum (22nd) and Stina Blackstenius (662nd) netting the Arsenal goals. Â
Hunt, Catley and Cooney-Cross all picked up yellow cards, among seven dished out.
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