Elsewhere, Liverpool Ladies clinched their first Women's Super League title by beating Bristol in the end-of-season decider.
The visitors started the match two points behind the Reds and needed a win to snatch the championship as the campaign went down to the wire.
But the hosts dominated from the start, taking the lead through a Louise Fors penalty after Nicole Rolser was fouled.
Katrin Omarsdottir's fine finish sealed the 2-0 win to end Arsenal's nine-year dominance in the women's game.
The Gunners won eight consecutive Women's Premier League titles from 2004 and finished top for the first two seasons of the WSL.
But these two sides usurped the Londoners to battle it out at the top of table all season, culminating in a winner-takes-all encounter at the Halton Stadium.
The triumph completes a remarkable turnaround for Liverpool, who finished bottom of the table for the last two seasons.
But after huge investment from the club's American owners, manager Matt Beard overhauled the squad for the 14-game league season and saw his side lose just twice.
The pre-match scenario invited comparisons with the dramatic finale to the men's First Division title in 1989, when George Graham's Arsenal travelled to Liverpool needing a 2-0 win, which they famously sealed with Michael Thomas's last-minute goal.
Any winning scoreline would have done for Bristol, but the hosts made the stronger start and the influential Rolser curled one effort over before being denied by a superb save from goalkeeper Siobhan Chamberlain.
It was no surprise when the German forward was involved in the opening goal, drawing a foul after twisting and turning in the penalty area, with Fors lashing the spot-kick past Chamberlain.
Bristol created a rare chance moments later when Laura del Rio tried to lob Rachael Laws, but although the Liverpool keeper was beaten the Spaniard's shot rolled inches wide.
The visitors have made a habit of coming from behind this season, but they struggled to break down Liverpool's defence as the Reds sat back after the break.
It was the home side who had the better chances on the counter-attack, with Amanda da Costa sending a simple header over the bar after finding herself unmarked 10 yards out.
The decisive second goal came 10 minutes from time when Natasha Dowie laid off a free-kick to Omarsdottir, who took a touch before rifling past Chamberlain from 15 yards.
Oh what woul Brendan Rodgers give to make it a club double come the end of the season? It is nearly 25 years since Liverpool last won the title.