Eddie May's tenure had begun on a bright note as his youthful side celebrated their first-ever game in Europe with a 1-0 win last Thursday.
But there was to be no such joy in the shadow of the Alps as they disappointingly exited the inaugural Europa League at only the second qualifying round.
Franz Burgmeier struck the 105th-minute winner to secure a deserved victory for the hosts after Emil Noll's goal levelled the aggregate score in the first half.
Last week's goalscorer Ryan Flynn dropped out with a slight strain and Chris Mitchell came in as part of a more cautious 4-2-3-1 line-up.
Vaduz coach Pierre Littbarski, the German World Cup winner, sent out the same team on home soil.
The neat Rheinpark Stadion welcomed around 1,000 Bairns fans who made their voices heard
before kick-off, despite the arrival of heavy rain and a blustery wind.
The early exchanges showed there was no love lost between the sides as tackles flew in - resulting in six first-half bookings - before Vaduz began to boss the action.
Throwing players forward in a flexible 4-4-2 formation, Pascal Cerrone sped in behind Darren Barr in the right-back position but his cross was gathered by Robert Olejnik.
Lively left midfielder Burgmeier then cut inside to flash a 25-yard drive just past.
The Bairns were struggling as Vaduz dominated, Damian Bellon next to see a shot deflected wide.
Olejnik was then called into meaningful action, clawing away a strike from Michael Stegmayer that was deflected en route by Nick Proschwitz. It was a smart save, even if the offside flag had been raised.
Burgmeier, the ex-Darlington player, was proving a nuisance and he was unlucky to see Marc Twaddle block another attempt for a corner.
But the red tide flowing towards the Falkirk goal claimed its reward on 24 minutes.
From yet another set piece, the Bairns failed to properly clear and centre-half Noll was able to turn Brian McLean and flick past Olejnik's despairing hand.
With conditions worsening as thunder cracked and lightning flashed, May's men were struggling to even move from their own half.
Bellon and Burgmeier again tried their luck from distance, the latter denied by a superb Olejnik stop. The Austrian keeper produced another excellent save to parry Bellon's long-range shot seconds from the break.
The pattern of play continued upon the re-start, Proschwitz seeing another shot deflected away.
Colocci then broke clear on the right and centred for the on-rushing Burgmeier who saw Olejnik spectacularly push over. Centre-half Marco Steil even stormed forward to try his luck from distance, seeking to emulate his partner Noll.
Flynn's arrival for Falkirk was welcomed, replacing Alex MacDonald, but the visitors still struggled for ball.
It was 76 minutes before the Bairns registered an effort and a chance it was. Burton O'Brien's corner landed at the head of Twaddle who nodded just wide.
Sub Dennis Kempe restored a familiar theme when Olejnik thwarted his fierce drive eight minutes from time before he wastefully fired wide at the end of normal time.
Flynn, set up by Scott Arfield, had a glorious extra-time chance but Peter Jehle made his first save of the contest.
It was to prove pivotal as Burgmerier won it, bursting forward and lashing in from 18 yards to secure a third-round meeting with Czechs Slovan Liberec.
Falkirk suffered further misery when Carl Finnigan was shown a straight red card at the final whistle.