New Zealand struggled for fluidity for a lot of the night, unable to reproduce the incisiveness in the attacking third that had highlighted the performance in Dublin.
Coach Danny Hay elected to use a completely different side to the one that had started against Ireland, which meant a central defensive pairing of Tommy Smith and Bill Tuiloma and a midfield trio of Michael McGlinchey, Alex Rufer and Matt Ridenton.
James McGarry was on debut at left back, while Elliott Colier made his first start for New Zealand.
Lithuania were coming off a miserable 0-6 defeat in Portugal, and hadn't won an international game for 18 months.
But they had played more than 15 matches in that time, and their combinations, as well as their physical size, meant it was never going to be an easy game.
In front of modest but vocal crowd at the LFF stadium, New Zealand made a nervy start.
Rufer was dispossessed in his own half after 15 seconds, and only a strong Michael Woud block prevented Lithuania from going ahead.
There was a further chance from the resultant corner, with the shot hitting the side netting.
The All Whites struggled to settle into the match; they tried to employ the same pass and move style that had been seen against Ireland, but couldn't get the same ball speed and rhythm.
It meant when the ball did come wide it was well covered, and the runs were predictable.
The artificial turf didn't help, as it is much less forgiving and the ball tends to run away from you rather than stick near your feet.
And this team had never played together, which meant the midfield trio of Rufer, Ridenton and McGlinchey were often making the same runs.
Ridenton was guilty of being caught in possession while Rufer was probably moving too much, instead of holding within a zone.
Tim Payne was dispossessed a couple of times on the right flank and basics such as throw ins were going astray early.
It was understandable to a degree, coming off a rushed trip to Lithuania and one brief training session, but it meant the All Whites was often under pressure, as the home side effectively utilized their high press.
There were a few chances. The best opportunity fell to de Jong, who clipped a shot from the edge of the area just over the bar with his weaker foot, after intercepting a stray pass from the Lithuanian keeper.
Marco Rojas, who was busy throughout, was just beaten to the ball at the near post, while a bullet Smith header was tipped over the bar by Ernestas Setkus in the Lithuanian goal.
But the men in yellow and green had many more opportunities, with Woud by far the busier custodian.
Tuiloma and Smith were forced into a series of last ditch blocks and tackles, with the home side missing some gilt-edged chances.
It looked like the All Whites would survive unscathed until halftime, but just like in Ireland last week, they conceded seconds before the break.
It was a beauty, a left foot rocket from right winger Arvydas Novikovas, who was probably the best on field.
It was struck from a full 25 metres, on the angle, and inside Woud's near post, after New Zealand had failed to clear the danger from a corner.
Hay brought on Joe Bell and Sarpreet Singh at halftime, for Rufer and Ridenton.
The duo brought measure of control in the midfield, with Bell in particular offering stability, while Singh created space for a couple of shots and showed vision with some raking passes.
But Lithuania always looked more likely, and Woud, who had almost been punished for some risky passes from inside his own area, made the save of the match with five minutes to play to deny Novikovas his second.
New Zealand 0
Lithuania 1 (A Novikovas 45)
Halftime 1-0
