New Bairns boss Eddie May's tenure began on a positive note as the home side celebrated the their first ever game in Europe with a win that just might be enough to see them through the second leg in Liechtenstein next Thursday.
After an unconvincing first half, winger Flynn, the former Falkirk academy player on a season-long loan from Liverpool, scored with a deflected drive five minutes after the interval.
It was a blow to the visitors who looked the more assured for long spells, but that will not bother May who got off to the best possible start after taking over from John Hughes earlier this summer.
Disappointingly, for such an historic occasion, there were only two stands open to house the crowd of 5,763 and the first half was rather subdued.
May gave debuts to summer signings Flynn, Brian McLean, Alex MacDonald and Marc Twaddle who was returning to the club for the second time.
However, there were long spells of tedium until the 29th minute when Vaduz midfielder Franz Burgmeier set up Kai Koitka with a clever reverse pass on the edge of the box, only to watch the German thrash the ball high over the bar.
Koitka was proving a handful down the Falkirk left but it was from a Michael Stegmayer corner moments later that he headed in to Robert Olejnik's arms from only six yards out after the Bairns keeper had flapped.
Vaduz, managed by former Germany international Pierre Littbarski, had the edge but it was certainly no European classic.
Two minutes from the interval the Liechtenstein side came close to getting the breakthrough when, from Stegmayer's long throw, striker Nick Proschwitz climbed high to head the ball inches past the far post.
Falkirk brought out a much-needed sense of purpose with them for the start of the second half, and in the 50th minute they took the lead when Vaduz failed to clear Scott Arfield's free-kick which was floated into the penalty area from 30 yards out.
The ball fell kindly to Flynn just inside the box and his quickly-dispatched drive took a deflection before it flew high past Vaduz keeper Peter Jehle.
The complexion of the game changed immediately and seconds later Arfield, buoyed and confident as he strode forward, sent a drive from 25 yards inches over the bar.
However, Vaduz upped the tempo and six minutes later, after an Olejnik error allowed Koitka to get in a header, Bairns' left back Tam Scobbie had to quickly clear the danger.
Moments later, captain Michael Stuckmann's drive from 20 yards was goal-bound until it struck Arfield and sped past the post, the home side surviving the corner.
Falkirk became increasingly nervous as Vaduz threatened to grab the away goal which would have turned the tie in their favour.
Vaduz threw on their three substitutes but aside from an injury-time drive from substitute Ando Farndic which went inches over the bar, they mainly huffed and puffed around the Falkirk box as the home side held on for the narrow win and vital clean sheet.