The Women's FA Cup final triumph completed a memorable end to the season for the Australian international, who only returned from a long-term knee injury in February.
She subsequently played a key role as City took the domestic Double having clinched the Women's Super League earlier in May - Fowler's first league champions' medal.
But it was a deflating day for Brighton manager Vidosic, though he can be proud of the way his team played for much of the club's first final.
They were far the better side for Sunday's opening half-hour and with better finishing could have sprung a shock. There is certainly much for this ambitious coach and club to build on.
Pre-match there was a touching tribute to Vidosic's father Rado, a well-known figure in Australian soccer, who died aged 64 in January.
Rado had been working alongside his son in England and as the teams lined up Brighton fans raised a giant tifo celebrating Rado, with his and Dario's faces on it and the words: FATHER, COACH, MENTOR.
"It was a beautiful thing to see, and a massive thank you to the club and the fans," said Vidosic.
"He would have loved to have been a part of today, but I'm sure he was in a way, he was probably at the best seat in the house, somewhere watching it, and he would have been really, really proud of the girls."
While Fowler began the match on City's bench her fellow Matilda, Charlize Rule, started for Albion and was quickly influential, stepping inside from right-back to rotate possession as the underdogs began confidently.
It was Rule, striding forward from defence, who created the first opening. She released Japanese striker Kiko Seiko who crossed for Fran Kirby only for the England veteran's close-range shot to be blocked.
Kirby, a five-time FA Cup winner with Chelsea, was the only Albion player with previous experience of the occasion but they were far from overawed. Former Sydney FC title-winner Madison Haley was a constant threat as Brighton created several decent chances.
However, their failed to convert them proved costly as City woke up.
After 37 minutes Lauren Hemp held off Rule and laid back to Alex Greenwood who delivered a hanging cross that Bunny Shaw rose above Chiamaka Nnadozie to head in.
Six minutes into first-half added time City had their second. Shaw was fouled after Albion failed to clear a City attack. Greenwood curled the free-kick past the goalkeeper's weak dive.
Albion had come back from 2-0 down to win at Liverpool in the semi-finals but doing so against the champions was another matter and both teams knew it.
City put the game to bed after 66 minutes. Shaw broke, the ball came to substitute Aoba Fujino who worked a yard of space before striking a deflected shot past Nnadozie.
With Rule off and Fowler on as both sides replaced tiring legs Vivianne Miedema added a harsh gloss to the scoreline as she headed in a fourth.
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