The Saddlers completed the double over Vale this season thanks to goals from Sam Perry and Emmanuel Osadebe.
It made it five victories from six home games for Flynn, and he said: "The work rate was superb.
"Even if we had lost that game, the way we worked and performed, it was pleasing to see.
"I've said before there are ways to win games, and when they put that commitment and effort in, we're a tough, tough team to beat."
Perry replaced Joss Labadie, who limped off injured towards the end of the first half, and met Osadebe's cross with a deft glancing header to open the scoring.
Osadebe put the result beyond doubt by slotting home in stoppage time.
"I was over the moon for Sam as we could've put someone else on – changed it and tweaked it around – but we wanted to give him his chance in a big game," said Flynn.
"He did very well, and the run he made for the goal, he got across his man and it was a good finish.
"I don't mind saying that's the best I've seen Emmanuel play.
"I thought he was superb. There are still one or two little things I want to get out of him, but he was superb.
"He had discipline and energy, and he scored and assisted. I can't ask for much more."
The travelling Vale fans made their voices heard but Walsall were also backed by a noisy home crowd, and Flynn loved the atmosphere.
He added: "We want to make it difficult. If teams are going to beat us here, I don't want it to be because of a poor performance.
"I want teams to come and earn the right for three points, and only one team has done that.
"We've won five out of six at home, and that is promotion form.
"The atmosphere was superb. I loved being manager here today.
"It helps when you win, but the Port Vale fans were loud, and our fans were even better.
"They were loud and got behind the boys. It was a hard-fought victory, and they're the pleasing ones."