Ji So-Yun's goal early in the first half saw the Blues take control of the game before Gilly Flaherty doubled their lead from a corner just after the hour mark, but Caroline Weir's calm finish gave the home side hope in the closing stages.
The result sees the visitors maintain their 100% winning record at the start of the new season, leaving Liverpool with four points from three games in a mixed start to the new campaign.
Three changes from each manager
Reds manager Scott Rogers made three changes from the side which drew three-all with Sunderland last time out, with Emma Lundh, Laura Coombs and Martha Harris dropping out and Mayumi Pacheco, Rosie White and Katie Zelem coming in.
The visitors likewise made three changes of personnel. Eni Aluko, Ana Borges and Jade Bailey started, with Claire Rafferty, Drew Spence and Karen Carney making way.
Tribute to Hillsborough victims
A minute's applause sounded around the ground ahead of kick-off in light of the recent ruling regarding the 96 Liverpool fans who lost their lives in the 1989 Hillsborough disaster. Poignant chants of "justice for the 96" could also be heard as the game kicked off.
Aluko had the first chance of the game for the visitors within 60 seconds of kick-off, but her right-footed shot from the edge of the area was weak and an easy save for Siobhan Chamberlain.
Weir forged herself an opening soon after with some neat footwork just outside the box, but her curling left-footed effort drifted across goal and comfortably wide.
Ji opens scoring with simple finish
The opener came after 14 minutes, as Blues star Ji siezed on a loose ball inside the area and calmly drilled a left-footed shot across the goalkeeper into the bottom-right corner.
Question marks were raised about the Reds' defending, with the South Korea international permitted ample time and space to place her shot under little pressure to notch her first goal of the campaign.
The hosts looked to hit back immediately through Katie Zelem as she broke into the area from the right wing, but Hedvig Lindahl got her body behind the shot and collected the ball at the second attempt with a Liverpool striker closing in.
Chelsea dominate possession and chances
The lead should have been doubled after 25 minutes as two Chelsea players somehow found themselves with yards of space at the edge of the six-yard box, but a breakdown in communications saw an attempted knock-down from Gilly Flaherty bounce disappointingly wide with the goal gaping.
Moments later, Weir found herself space once more with a delicate spin inside the area but saw her driven shot well saved, before Blues captain Katie Chapman hacked the ball off line from the resulting corner.
Chelsea were on top, however, and went close throug a deflected Fran Kirby shot and a cross from Aluko which Chamberlain only just managed to smother at her near post with Kirby lurking with intent.
Blues captain forced off on brink of half-time
There was a break in play on the 40-minute mark as Blues captain Chapman received lengthy treatment after a blow to the head inside the centre circle. Thee 33-year-old was visibly groggy as she was forced to withdraw from the action, with Bethany England coming on as her replacement.
Gemma Davison bent a right-footed shot just shy of the far post from the corner of the penalty area in what was the last meaningful action of the first period, with the two sides going in for half-time to a warm reception from both sets of fans.
Bailey drew a strong save from Chamberlain early in the second half as a loose ball came to her at the edge of the area and she fired towards the top corner, with the visitors looking to continue their first-half dominance.
Within the next five minutes, Kirby hit a bobbling shot just wide of the post from a tight angle and England blazed over the bar from range as Liverpool struggled to maintain any meaningful spells of possession.
Chelsea double lead as Liverpool waste chances
There were two golden chances within the space of 30 seconds as Weir and Kirby were released through on goal at either end of the pitch, but neither international could evade the attention of the opposing defence long enough to take advantage.
Liverpool had another good opportunity on the hour mark as Dutch winger Shanice Van De Sanden was released down the left, but her eventual shot hit the side netting just outside the post as she looked to finish from a difficult angle.
The hosts were made to pay for their profligacy almost immediately as Ana Borges' corner was nodded on by substitute England and Flaherty was on hand to steer a header in at the back post.
Chelsea wee forced into another change with 20 minutes to go as goalkeeper Lindahl went down with a head injury, with Becky Spencer coming on as her replacement.
Reds claw their way back in late on
Some in the stadium thought Liverpool had a goal back as a deflected cross bounced over the substitute keeper Spencer and Weir looped a header up, but she failed to connect properly and the ball dropped across the face of goal and away.
Just a few minutes later, Weir had her goal and Liverpool their route back into the game. Charles fed her down the left with a clever pass and the number 10, arguably the Reds' best performer on the night, made no mistake as she drilled a left-footed shot under the keeper and into the far corner.
Charles drew the best save of the game from Spencer in the 90th minute after flicking a close-range volley towards goal, before yet another clash of heads from the corner which followed meant that further time would be added onto the eight minutes of stoppage time already signalled.
Mandy Van Den Berg's long ball forward almost drifted into the net deep into stoppage time, but both Spencer and Chelsea held on to claim a third successive victory in the WSL.