Flynn saw his mid-table side move four points clear of his former team Coleraine after the victory, in which three players were sent-off.
He added: "I'm leaving with a very heavy heart. I can assure you that I'm leaving a club that I don't want to leave and I'm absolutely gutted.
"I made my mind up before the Ballymena game on Saturday.
"I made the Chairman aware of that by email and no matter what the result had been tonight, I was always stepping down.
"The one thing I asked when I came down here was respect for everyone within the club, from the ground staff to the tea lady, and I always had that drilled into the players.
"I can look at everyone at this club and say that I've given 100 per cent."
Flynn guided Newry to the Co-Operative Cup final last season, losing out 1-0 to Portadown in the Mourneview Park decider.
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