After their comprehensive 4-0 win on the opening day of the season - this success was at the other end of the spectrum as Flynn's men were forced to dig deep for large spells in the game to make it back to back victories.
The Exiles were much the better side in the first period, hitting the post before being denied a certain goal when Peter Clarke hooked the ball off the line late in the first period.
Then despite having hardly had a sight at goal all afternoon, they were ahead just after the hour mark when a Taylor Allen corner looked to have been scrambled home by Andy Williams - however it went down as a Mickey Demetriou own goal.
Flynn's men then had to withstand a barrage of pressure - which was ramped up when Allen was handed his marching orders for a second booking.
The bombardment from Newport kept coming - but Walsall scrapped and headed everything clear, holding firm for a second successive win.
It won't be remembered as one of the most pretty victories of the season - but it could turn out to be a hugely important one just two games into the campaign.
As expected Flynn decided to stick with the same side that put Hartlepool to the sword on the opening day of the season - with striker Tom Knowles named on the bench after arriving from Yeovil Town in mid week.
The Saddlers boss was given a warm welcome from the Rodney Parade crowd - having earned hero status during his four year spell at the club after leading them to string of cup giantkillings and two play off finals.
But after the handshakes and embraces with the Exiles staff it was down to business - as his side looked to continue where they left off on the opening day.
However, it it was evident early on that it wasn't going to be as simple as it was last week at the Poundland Bescot Stadium - with Newport putting Flynn's men on the back foot almost from the off.
Isaac Hutchinson did see an early free kick sail over for the visitors - but the Exiles then got on top and after ten minutes it looked as if they had broken the deadlock.
Aaron Wildig rose highest to meet a left wing cross and head home past Owen Evans - only for the linesman to raise his flag for offside.
Minutes later Declan Drysdale's header from a long Mickey Demetriou thrown in came back off the upright - with Evans then palming away a rasping effort from Matt Dolan
The Saddlers goal was leading a charmed life as the pressure kept coming and when Offrande Zanzala went down in the box following a tangle with Donervon Daniels - the Rodney Parade crowd wanted a penalty but the strong calls fell on deaf ears as referee Ollie Yates waved away the claims.
Flynn's men were trying to get the ball down and get a foothold in the game - but the home side just weren't allowing that to happen, regularly turning over possession and looking dangerous going forward.
Sam Bowen's curling effort from 18 yards flew inches over the Walsall crossbar midway through the half - before the Saddlers did carve out a rare chance against the run of play.
Liam Kinsella sprung the offside trap down the right to cross for Andy Williams - but he couldn't adjust his feet and get a clean connection on the ball. That rare opportunity did little to turn the tide of the half as County kept coming forward.
Demetriou's long throw ins were proving difficult to handle - with one whistling across the six yard box late in the first period, before a ditch clearance from Peter Clarke kept it level at the break.
Dolan's deep cross from the left was met by Zanzala whose header looked set to cross the line but for veteran defender Clarke, who scrambled back to hook the ball clear.
After being on the back foot for must of the first half Flynn will have hoped after re-grouping at the break his side would emerge for the second period and gain the upper hand themselves.
But that failed to happen in the opening 15 minutes - forcing the Saddlers boss into a double change as Timmy Abraham replaced Danny Johnson and Tom Knowles was handed a debut in place of Hutchinson.
Then, just minutes after the substitution, they found themselves in front.
Taylor Allen's deep corner from the left was headed towards goal with a scramble in the six yard box ending with the ball in the Exiles net, courtesy of a final touch from Williams.
It was Walsall's first real clear cut chance of the game - but somehow they were in front.
But again the goal didn't turn the tide of the game - as Newport went in search of an immediate response and they should have been level 22 minutes from time.
Demetriou's dangerous long throw was again the key weapon, as he launched it into the box and a flick on fell to the unmarked Declan Drysdale but ballooned the ball over from eight yards out.
The Saddlers back line, marshalled by Clarke, was having to soak up sustained pressure as Newport continued to look dangerous going forward, pumping a number of balls into the box.
Then the visitors were dealt a big blow six minutes from time when Allen was handed a second yellow card after a coming together with a Newport player- and that had come after the home side were getting increasingly frustrated with niggling fouls from the visitors.
With Walsall down to ten the pressure ramped up even further, as Newport continued to knock on the door time after time.
Demetriou dragged an effort wide but that was about as close as the home side came late on despite their pressure - with Walsall's back line holding out for the three points.
Newport County: (3-5-2) Townsend, Drysdale, Dolan (Waite 69), Demetriou, Norman, Wildig (Collins (80), Bowen (Aaron Lewis 69), Bennett, Evans (Adam Lewis 83) Bogle (Zimba 83), Zanzala
Subs not used: Day, Willmott
Walsall: (3-4-1-2) Evans, Daniels, P. Clarke, Monthe; White, Kinsella, Comley, Allen, Hutchinson (Knowles 61), Williams (Earing 83), Johnson (Abraham 61)
Subs not used: Przybek, James-Taylor, Maher, Bennett
Goals: Demetriou OG, 63
Referee: Ollie Yates