Kelly Smith inspired the club's 13th victory in the competition, scoring the first and setting Yukari Kinga's second at stadiummk.
And the result meant a winning farewell for boss Kerr, who announced her intention to leave last week with the club bottom of the FA Women's Super League 1 table.
In a repeat of the 2010 final, Arsenal quickly asserted their dominance and a 10th-minute thunderbolt from Rachel Yankey cannoned back off the inside of the post.
Smith screwed her shot wide when unmarked in the box less than a minute later but England's record goalscorer quickly made amends.
A foul by Toffees left-back Alex Greenwood on 15 minutes gave her the chance from a free-kick and she curled an unstoppable 20-yard effort into the left-hand corner of Rachel Brown-Finnis' goal.
After half-time, the Gunners picked up where they left off as Smith's 20-yard curled effort rebounded off the woodwork.
The 35-year-old then turned provider on 61 minutes as Arsenal grabbed a deserved second - Japanese international Kinga calmly placing Smith's lay-off into the bottom corner from 12 yards - before Emma Mitchell hit the bar in the dying seconds.
Kerr paid a glowing tribute to Smith afterwards, although she was quick to dedicate the victory to an all-round team effort.
"It was never about me today, it was all about the team," said Kerr. "They focussed all week on their preparation and they showed their talent and got what they deserved.
"Kelly Smith is just incredible - she's 35 years old and you guys in England will never see another player like her, she's so talented.
"Kelly has been outstanding - she's a fantastic leader who leads by example on and off the pitch.
"I'm going to have a couple of weeks off now, relax and evaluate and have some time off."
Everton boss Andy Spence added: "When you give away a free-kick in the type of area that we did then with Kelly's world-class quality you're always risking the chance of conceding and to be fair to her she's scored a fantastic goal.
"The way the teams were balanced I thought whoever scored the first goal would go on to win the match and it transpired to be that way.
"Although it's disappointing now, it's important that we learn from this experience and we use it when we come back to cup finals in the future."