Hayden White levelled for the Saddlers after they fell behind early on - before Danny Johnson popped up in injury time to grab the winner.
Flynn, who insisted the visiting stopper was man of the match after denying his side on a number of occasions, said: "It was well deserved overall even though they had to play with ten men for a long time we were the better team and I am delighted we could get the win.
"We switched off a little bit for their first goal and it was good strike by Dominic Telford - I know what he can do having worked with him at Newport and he enjoyed that one going in.
"But I was pleased with the way we got back in it straight away which was pleasing.
"I made their goalkeeper the man of the match for some world class saves in the second half and we had untold amounts of pressure then and something like 24 shots in the whole of the game.
"But it took that little bit of finishing skill to win it for us in injury time and credit to Danny for that- again it was a great finish.
"It was a good crowd today for a good, exciting game, if nervy for the managers at time and hopefully they will have seen things there that make them want to come back again."