Jonas Eidevall’s side trailed within two minutes when Sam Kerr headed Chelsea in front but the Gunners responded and were much the better side at Selhurst Park.
Buoyed by a strong Arsenal following among a record crowd in London, they outplayed and outwitted their long-standing rivals to claim a sixth League Cup.
Striker Stina Blackstenius calmly slotted in the equaliser after Kerr’s opener, before Arsenal captain Kim Little netted from the penalty spot to make it 2-1.
The Gunners continued to dominate, although the combination of Kerr and midfielder Guro Reiten provided an ongoing threat for Chelsea, and Eidevall’s side extended their lead on the stroke of half-time when the ball deflected off Blues defender Niamh Charles and into her own net from a corner.
It is a huge result for Arsenal and coach Eidevall, who has won his first trophy with the club and ended a significant period without silverware for a side who had previously dominated English women’s football.
“These are the games we want to play,” Eidevall told BBC One.
“To get results creates belief. It was really important to get that reward and now we can be filled with belief for all the games going forward.”
Chelsea, on the other hand, have now suffered defeat in back-to-back League Cup finals despite winning three successive Women’s Super League titles.
Hayes said: “Everything has to be top class and today it was not at Chelsea standard. Sometimes you have to lose games like this to be reminded.”
Significant win brings back memories of Gunners’ golden era
And it was Chelsea’s supremacy in this fixture – and in domestic cup finals – which dominated the pre-match build-up.
Eidevall’s tactics were planned to perfection as his side tore through Chelsea in the first half, using width to great effect and showing a steely side they have missed on too many occasions this season.
Blackstenius, criticised of late for her lack of ruthlessness in front of goal, answered her critics with a composed finish for the crucial equaliser and the outstanding Little also got on the scoresheet.
The third goal sealed the win on the stroke of half-time and Arsenal showed resilience to hold on after the break, reminiscent of their successful teams of old.
“We had to break the chain at some point and today was that day,” Leah Williamson, the Arsenal defender and England captain, said.
“It meant a lot more to us. Arsenal should be winning trophies and that started again today.”
There were jubilant scenes at full-time as Arsenal’s players ran hand-in-hand to their supporters to celebrate as ‘Sweet Caroline’ rang out at Selhurst Park, where the 19,010 in attendance beat the 8,004 record set at last year’s final.
Chelsea, who are not used to losing, threw everything at Arsenal in the final 10 minutes but could not find a breakthrough and will return their attentions to the WSL and FA Cup, hoping to defend both titles.