A solitary goal from the midfielder was enough to wrangle top spot in Group B from Diego Simeone's men who were distinctly average on a chilly night in the Czech Republic
The game-winning goal was scored midway through the first half, as Vaclav Prochazka took advantage of some poor defending to stab the ball into the net from close range.
Atletico were rarely in it, as they were bettered for large periods of the encounter. Diego Costa would compound their misery with a red card in the 90th minute as they ultimately suffered their second European defeat in three games following a 15-game winning run in the competition.
Diego Simeone's side retained only three players from the side that lost 2-0 to Real Madrid, as his second-string side graced the Europa League once more, with the likes of 18-year-old Javi Manquillo handed his European debut.
The Czech side started favourably in below-freezing conditions, as they carved out the first real chance of the game. Frantisek Rajtoral skipped past his marker with ease, before sending a lofted ball into the box, as Marek Bakos headed somewhat tamely at Sergio Asenjo.
The visitors were distinctly second best in a closely fought opening period, though Juanfran's mazy run down the right flank saw Adrian fail to seriously trouble Matus Kozacik with a poor finish.
Viktoria did take the lead though, a testament to their comfortable opening in the Czech Republic. Atletico failed mark Vladimir Darida's inswinging corner adequately, with Prochazka latching on to a deflection to fire home after 26 minutes and seal his first goal in European competition.
The Spanish side were struggling to penetrate a resolute Viktoria defence, though when the chance presented itself, Simeone's men just couldn't capitalise. Radim Reznik allowed Diego Costa to expertly control a through ball in space, though his angled effort was well saved by Kozacik as the first half ended in the hosts' favour.
The second half began in an equally scrappy manner, as the Czech league leaders continued to frustrate their opponents and assert their authority. Emre's free-kick in a promising position deflected off the wall, as the visitors continued to seek an equaliser.
Atletico did demonstrate signs of resurgence, as Simeone opted to bring on Koke, and within seconds, the 20-year-old had a telling impact as he evaded the challenge of Reznik, before launching a fierce strike which only just cleared Kozacik's bar.
Pedro Martin bundled in an equaliser with a minute to play, before the goal was ruled out due to a foul in the build-up. In the ensuing aftermath, Diego Costa was shown a red card for pushing over a player as Simeone's side ensured it would be a night to forget.
Viktoria would hold on to seal the victory which would confirm them as Group B winners, one point ahead of Atletico, with the draw for the last 32 scheduled for next Friday.