It was the first time Flynn had returned to the club where he had enjoyed four and a half successful years - guiding the club to two play off finals while enjoying memorable FA Cup scalps, before stepping down in October 2021.
A second half own goal from Mickey Demetriou proved to be the difference between the two sides - despite the Saddlers having to withstand long spells of sustained pressure from the home side.
Flynn praised Newport and insisted his former side deserved to win the game - but hit out at a section of Exiles fans for 'absolutely disgusting' comments directed at him regarding his wife.
Flynn said: "I had some very unsavoury comments talking about my wife which I thought was a disgrace after everything I have done for this football club, to call my wife those, and I am not even going to repeat it, it was an absolute disgrace.
"I don't mind the usual banter as they say, but to be abusing my wife in the crowd was absolutely disgusting, it probably makes the win a bit sweeter after those comments.
"They overstepped the mark, it just shows what lowlife they are really, if they think that's acceptable, I don't care what they say about me because you are going to get abuse everywhere, but don't bring people's partners into it.
"I wish those comments hadn't come and I wish Newport well."
Flynn also alleged that stones were thrown towards the dugout.
He added: "It wasn’t just insults, stones were getting thrown by the supporters behind [the dugout].
"I can take abuse towards me but when they start bringing my wife into it and throwing stones, it’s not good.
"I’m not going to make a complain, I don’t want Newport to get in trouble.
"I’d probably just say have a look at the CCTV and ban the clown who did it – simple."
Newport hit the post and had one cleared off the line in the first half - before laying siege to the Walsall goal after Taylor Allen was given a red card for two bookings late in the game.
But Walsall's back line stood up to the test although the Saddlers boss did admit 'the better team lost'.
He added: "I know more than anything what a tough place this is to come, I thought Newport were very good today and I don't mind saying the better team probably lost.
"They are on a bad run of form at the minute, I think if they keep playing way they did today they will beat a lot of teams here, but I wanted to give the opposition credit, because I thought they were good today.
"Us, we dug in, we were solid, but were weren't very good with the ball at all, didn't create much at all, so it is very pleasing to get a clean sheet and the three points because as good as we were last week, we were nowhere near as good today, but we have managed to get the win and that is an important way to win games.
"It is an ugly win - it is a bittersweet moment if I am honest, because I have never wanted Newport to lose before, so it is a strange one, you can't have it every way, we got the points and we are buzzing to have another clean sheet."