Crusaders will be looking to progress to the second qualifying round of the Europa League after beating Ekranas in Thursday's first leg at Seaview.
Crues new boy Stephen Cockcroft put the Belfast side ahead in the 23rd minute and Jordan Owens scored a close-range header just before the interval.
Skipper Colin Coates pounced to head in the third on 58 minutes.
However, the Lithuanian side grabbed an important away goal through Aleksander Susnjar's 88th-minute header.
That late goal will have dampened the celebrations in the Crusaders camp as a 2-0 home win for the Ekranas in the return leg on 10 July would take the Lithuanian side through.
Twenty-year-old Cockcroft - just signed from Championship side H&W Welders - tapped in the opening goal after Declan Caddell bundled his way into the box to set up the easy chance.
Owens pounced to make it 2-0 just before half-time. Craig McClean crossed, keeper Kornelijus Timofeyevas misjudged the flight of the ball and was left stranded, leaving Owens to easily head in from close-range.
After a period of sustained pressure from the visitors, Crusaders captain Colin Coates put his side 3-0 up.
From a Cockcroft corner, Chris Morrow chested the ball down and shot from the edge of the 18 yard box. The keeper parried the ball and Coates was in the right place to head in from six yards.
Susnjar headed in the valuable away goal after a Dovydas Norvilas corner was punched by keeper Sean O'Neill but the Crues failed to complete the clearance.