The Gunners have now closed the gap to just one point behind the third-placed Reds in the table.
Ahead of the clash at the Select Security Stadium in Widnes, Scott Rogers was dealt a pre-match blow with the news goalkeeper Siobhan Chamberlain was absent through injury - and he was also without Amy Turner, who picked up a knock during Sunday’s FA Cup win over Watford.
Therefore, Becky Flaherty started in goal while another talented youngster from the development squad - Ali Johnson - was also in the XI. New signing Rinsola Babajide was on the bench for the first time.
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After early possession from Arsenal, Liverpool Ladies carved out a decent chance on 10 minutes. Good pressure from Johnson down the left flank saw the ball fall to Jess Clarke in the penalty area. After her path to goal was blocked, the loose ball broke for Bethany England, but she drove an effort over the bar.
Then, on 16 minutes, Liverpool Ladies almost tallied a goal-of-the-season contender when Caroline Weir turned past two Arsenal players and from 35 yards out spotted Gunners stopper Sari Van Veenendaal off her line, but could only watch her audacious chip come back off the bar.
However, around the half-hour mark Arsenal took the lead from the spot. Sophie Ingle brought down Vivianne Miedema, although the challenge appeared to be outside the penalty area. Despite furious protests from the Liverpool players the referee gave a spot-kick and though Miedema’s initial effort was brilliantly saved by Flaherty, the Arsenal No.11 put away the rebound.
A minute before the break it was 2-0 via a fine finish from Dominique Janssen. After the visitors hit the post following a corner, the ball came out to the left edge of the penalty area, and Janssen curled into the top corner.
The strike was the last kick of the opening half and it was perhaps tough on Liverpool Ladies, who had played well and were unfortunate not to have found a goal for their efforts.
Despite losing the second goal right on the stroke of half-time, Liverpool Ladies continued to try to take the game to Arsenal in the second half. Laura Coombs tried her luck from distance with a swerving effort that just cleared the bar.
The hosts had begun brightly following the re-start, but Arsenal made it 3-0 when Lisa Evans produced an emphatic finish from close range after a sweet one-two with Heather O’Reilly.
At the other end, Casey Stoney struck the post at a corner, while Rogers also handed new signing Babajide a debut when she appeared for the final 10 minutes of the game.
Liverpool Ladies next face another tough clash at the weekend as they head to Women’s Super League leaders Manchester City on Sunday.
Reflecting on the 90 minutes, Rogers told Liverpoolfc.com: "At the end of the day they took their chances and we didn't, and sometimes you just have to say that's football.
"In the first half we had a few good chances and if we had put them away then I think we would be talking about a completely different game.
"The penalty was a game changer unfortunately as we thought [the challenge] was outside the box."
Liverpool Ladies: Flaherty, Harris (Hodson, 70), Greenwood, Stoney, Ingle, Johnson (Murray, 63), Longhurst (Babajide, 80), Coombs, Clarke, Weir, England.
Subs not used: Ramsey (GK), Rogers, Roberts.