Thirty-seven-year-old Flower, brother of England batting coach and Zimbabwe exile Andy, scripted a composed chase of 215 after mid-innings collapse left his side in a spot of bother at 93/4.
He remained undefeated on 70 as Essex gained revenge for defeat to Kent in the semi-finals of the Twenty20 Cup last month.
When Essex lost England pair Ravi Bopara and Alastair Cook in consecutive Robbie Joseph overs, momentum appeared to be switching towards Robert Key's team.
But Zimbabwean Flower milked the ball in the gaps and shared a 68-run stand with England discard stumper Jamie Foster.
Flower despite a mid-innings slump kept Essex in pursuit as he did not allowed requiredrun-rate get much beyond five per over.
Flower, who nudged, cut and dabbed his way to a 73-ball 50, fittingly sealed the much-deserved win by lofting a full toss from Azhar Mahmood over mid-on for four.
Former Pakistan all-rounder Mahmood earlier struck twice during the powerplay overs to keep Kent in hunt, removing openers Mark Pettini and Jason Gallian in two separate spells.
Essex set off at a gallop in pursuit of their target but were checked when Mahmood, from the nursery end, trapped captain Pettini in front of the stumps.
Veteran Gallian, who struck some crisp early boundaries, then followed when Mahmood, having switched to the pavilion end, was bowled via an inside edge.
Cook and Bopara attempted to steady things but the loss of the latter to a contentious leg before wicket threw the game back into the balance.
Joseph's first over of a new spell resulted in Bopara being struck high by a delivery of extra bounce which appeared to be passing over the top of the stumps.
Left-hander Cook then perished in a soft manner as he poked a Joseph long hop into the covers, where Darren Stevens stooped to complete the dismissal.
Essex might have been chasing a less substantial target but for a late injection of runs from Ryan McLaren, one of Kent's South African contingent.
His classy 63, which was terminated by the final ball of the innings, was the only other innings of substance after Martin van Jaarsveld extended his extraordinary form in this year's competition.
van Jaarsveld, 34, came into the contest on the back of 602 runs in just eight FPT matches.
He added another 58 to his tally to counteract a successful start by the Essex pace attack.Arafat contributed with little cameo down the order as Kent put on a fighting 214 despite initial hiccups.
Kent 214 all out in 50 overs (van Jaarsveld 58, Ryan McLaren 63, yasir Arafat 23; Masters 2/34, C Wright 2/36,Danish Kaneria 2/42,Ravi Bopara 2/46) lost to Essex 218/5 in 48.5 overs (Grant Flower, ten Doeschate 30, Alistair Cook 33; Azhar Mahmood 3/40)