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The first chance of the game fell to the visitors, who saw Jasmin Kurtic blast a long-range effort wide in the fifth minute.
Both sides traded chances at an even rate in the early stages of the game, with Deivydas Matulevicius's chance in the 20th minute flying just wide of the right-hand post.
The 35-year-old, who plays for Shimizu S-Pulse in Japan, then doubled his side's lead when he smashed home from close range into the top of the Lithuania goal just four minutes later.
Igoris Pankratjevas's charges set about trying to address their two-goal deficit in the second half and stepped up their attacks, Gediminas Vicius and Arvydas Novikovas threatening Samir Handanovic's goal early on.
Arturas Zulpa then forced a save from the Slovenia keeper just after the hour, but as time ticked on, chances became more at a premium, as the visitors sought to take the sting out of the game.
Mikoliunas and Novikovas had further chances on goal in the last 10 minutes of the match, but ultimately, Slovenia managed to see off their opponents and secure all three points.