Excellent goals from Guro Reiten and Ji So-Yun booked the Blues place into the showpiece event at Wembley Stadium where they will take on Manchester City.
With these two sides going head-to-head in the Women's Super League (WSL), it was set to be a very exciting contest at Meadow Park.
In the WSL, both have played 18 games and are separated by just one point, with Hayes' team currently on 44.
And in the cup contest, these two sides showed the quality that has placed them first and second in the league.
However, the hosts, supported by their fans at the home of Boreham Wood FC, were made to pay for not taking the chances they had in the first half and in the second whilst the game was still goalless.
Stina Blackstenius received the ball on the left channel before making her way into the penalty area.
She rounded goalkeeper Ann-Katrin Berger, but no Arsenal player got on the end of the cut back and Chelsea were able to clear.
Vivianne Miedema also came close when her effort from range was slightly too high.
But in the second half, the best chance for the hosts came to Beth Mead who may struggle to sleep tonight.
An excellent ball from the left by Stephanie Catley was taken down by the Gunner number nine who did the hard part by taking the ball in and turning her marker.
With only the keeper to beat, the 26-year-old could only send her effort wide of the left post.
It was a guilt-edged chance, and if that miss wasn't big enough, it was amplified a minute later.
Reiten received the ball left of the goal and drove forward, and with no Arsenal player closing the Norwegian down, she decided to try her luck from range.
And her decision to go for goal proved to be the right one as she found the top right with a stunning effort from 25 yards out past Manuela Zinsberger.
Speaking on talkSPORT Courtney Sweetman-Kirk spoke about the quality of the strike how Arsenal would be made to rue the chances they missed.
"What a brilliant finish that is, I said before the game Guro Reiten could be an unsung hero, but she's been front and centre [today] and rightly so," the Sheffield United striker said.
"I said if Arsenal don't take their chances they will rue their chances.
"And a minute later after Beth Mead's miss they go up the other end and score".
The Blues would then put the tie to bed 11 minutes later when Ji scored an equally impressive goal.
Following a long ball into the box, Arsenal failed to clear their lines, and after the ball broke to the edge of the penalty area, the South Korean midfielder made the hosts pay.
She rounded Lia Walti, and even though the goalkeeper wasn't in the best of positions, Ji still had a lot to do to find the top right corner.
But she did, and Sweetman-Kirk had nothing but praise for the goal.
"We were questioning Zinsberger for the first shot, but there is no saving this.
"But there's a mix up defensively and Arsenal don't clear their lines.
"What a fantastic finish that is, and the area she hits it in, it doesn't get more into the corner than that".
The hosts tried to get back into the contest, but were unable to penetrate the Blues' defence as they now hope to retain the cup for a second successive season when they take on Man City on May 15.