Striker Kelly Smith scored an early opener before setting up Yukari Kinga to seal the victory on the hour mark.
Kerr resigned a week ago with her team bottom of the Women's Super League.
However, they looked anything but relegation candidates as they avenged their 2010 final defeat by the Toffees to lift the trophy for the 13th time.
Kerr quit last Sunday in response to the Gunners' poor start to the season - they have lost three of their opening four league games and are bottom of the table with a solitary point.
But she opted to stay on for this match at Stadium MK as Arsenal looked to add to a tally of 40 major trophies since they were formed 27 years ago.
They entered the match as favourites, in no small part because of their impressive record of 12 victories from their previous 13 appearances in this fixture but Everton four years ago being the only side to beat them in the final.
And the Gunners, league title winners in nine of the past 10 seasons, lifted yet another trophy in front of a crowd of just over 15,000 fans in Milton Keynes.
Arsenal celebrate winning the FA Cup Arsenal added a 13th FA Cup to 12 Premier League titles, two Super Leagues and a Champions League