Flynn marked his return to Falkirk with a decisive goal
Falkirk won their first ever match in European competition thanks to a debut goal by Ryan Flynn.
Flynn, who rejoined the Bairns on loan from Liverpool, struck five minutes into the second half to gain a first-leg advantage in the Europa League tie.
Nick Proschwitz had earlier come close for Vaduz with a header from Michael Stegmayer's throw-in.
Vaduz applied more pressure after the break and Tam Scobbie and Scott Arfield made crucial blocks for Falkirk.
The Bairns were being managed for the first time by Eddie May, who was promoted from coaching the reserve team after John Hughes left to join Hibernian.
And last season's beaten Scottish Cup finalists included Flynn and fellow new signings Brian McLean, Alex MacDonald and Marc Twaddle in their starting line-up.
Liechtensteiner side Vaduz arrived at the Falkirk Stadium having suffered relegation from the Swiss Super League into the Challenge League at the end of last season.
There were few chances in a quiet first half with Burton O'Brien's shot for the hosts saved by Peter Jehle on the quarter-hour mark.
Vaduz threatened twice through Kai Koitka with the midfielder firing over before heading into the arms of Robert Olejnik.
Falkirk captain Darren Barr was penalised for a challenge on Proschwitz, who headed over the resulting free-kick delivery from Franz Burgmeier.
The visitors continued to exert their authority in the match and almost broke the deadlock shortly before the break.
Stegmayer's throw-in from the right was flicked on by the head of Proschwitz and dropped just wide of Olejnik's far post.
Carl Finnigan tries to escape the challenge of Vaduz defender Emil Noll
The hosts won a free-kick early in the second half after Emil Noll impeded Carl Finnigan and the Vaduz defender was booked for tussling with the Bairns striker after referee Damien Ledentu had blown for the foul.
Arfield's cross was cleared by Koitka to the edge of the box and former Falkirk academy winger Flynn side-footed into the top-left corner of the net with the aid of a deflection.
Falkirk continued to press and Arfield fired narrowly over from long range.
Vaduz went in search of an equaliser and almost benefitted from a mistake by Olejnik after the keeper missed a cross and allowed Koitka to get in a header but Scobbie was on hand to make the clearance.
Michael Stuckmann then saw his goal-bound shot cleared past the post by Arfield.
Stegmayer's attacking prowess continued to cause Falkirk problems and the his cross was headed off-target by substitute Anto Franjic.
Vaduz pinned Falkirk back in the closing stages but could not find a breakthrough with Franjic's late drive missing the bar by inches.
But the Bairns are in good shape for next Thursday's return leg of the second round qualifying tie at the Rheinpark Stadion.
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