South Korea forward Ji So-Yun put Chelsea ahead with a low first-half strike and Gilly Flaherty's header from a second-half corner made it two.
Liverpool went close through Katie Zelem and eventually pulled a deserved goal back through Caroline Weir.
But Chelsea held on to inflict a first league defeat of 2016 on Liverpool.
The defending champions had looked comfortable when Flaherty, who signed a new two-year contract earlier on Wednesday, nodded in their second.
But Chelsea goalkeeper Hedvig Lindahl, who had done brilliantly to deny Weir before the break, had to be withdrawn after taking a knock.
Her replacement, Rebecca Spencer, then produced a superb reaction save to keep out Niamh Charles' late effort.
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Liverpool boss Scott Rogers told BBC Radio 5 live sports extra: "I thought we deserved a point. I'm delighted with the performance.
"They (Chelsea) are the champions for a reason. They've probably not performed at their best but they've still managed to win the game.
"They're a top class team and we've caused them a lot of problems tonight."
Chelsea Ladies boss Emma Hayes told BBC Radio 5 live sports extra: "Credit to Liverpool. I thought they deserved something from the game.
"It just showed how much work we're going to have to do, if we're to progress any further. We lacked experience in the middle of the park."
Chelsea Ladies moved back to the top of Women's Super League One as they made it three wins from their first three matches by beating Liverpool.