(Aggregate 4-4: Rhyl win on away goals)
Rhyl became only the second Welsh Premiership side to win a European tie after beating Atlantas on away goals in the Uefa Cup first qualifying round.
Gary Powell (right) scored the second crucial away goal
The north Walians lost the return leg 3-2 in Lithuania, but Gary Powell's 60th-minute strike proved crucial.
Atlantas took a 12th-minute lead through a Dainius Zernys penalty, but Greg Stones then brought Rhyl level.
Aivaras Laurisas and Andrius Peterikis struck for the home side after Powell's goal, but the Lilywhites held on.
The match ended amid ugly scenes as Atlantas manager Vacys Lekevicius raced onto the pitch and clashed with Morgan and goalkeeper Gerald McGuigan in the centre circle.
"It was a bit intimidating to be honest seeing the manager charging towards us," McGuigan told BBC Wales Sport.
"What was more frightening was that no-one stopped all their fans jumping over the barriers.
"It was a situation of getting into the changing rooms as quickly as possible."
Atlantas had played the majority of the game with 10 men after Zernys was sent off for a horror tackle on Rhyl's Alan Morgan three minutes after scoring.
Rhyl will now be in the hat for Friday's second qualifying round draw in Nyon.
The first leg of the second round will be held on 11 August, with the second leg played a fortnight later.
FK Atlantas: Briaunis, Deveika, Tolis, Bartkus, Lapeikis, Zukauskas, Petreikis, Navikas, Zernys, Ringys, Ksanavicus.
Subs: Lekevicius, Maciulevicius, Labukas, Zvingilas, Sarunas, Grigaitis, Ramonas.
Rhyl: McGuigan, Adamson, M Powell, Horan, Stones, Brewerton, Graves, Limbert, G Powell, Moran, Morgan.
Subs: Taylor, Thompson, Gatfield, Mutton, Davis, Connolly, Billingsley.
Referee: Lasha Silagadze (Georgia)