Naismith claimed the only goal of the game after skipper Darren Fletcher was denied from the penalty spot.
The Scots held on for the victory which sees them now sit two points behind the Czech Republic with two games to go as both nations battle for a play-off spot.
As well as the disappointment of being held to a 2-2 draw by the Czechs on Saturday, Craig Levein also had selection problems to contend with ahead of this match.
Kenny Miller and Scott Brown were both suspended, while Barry Robson and Charlie Adam missed out through injury.
That meant first competitive starts for David Goodwillie, Barry Bannan and Don Cowie, with Steven Whittaker returning from a ban to take his place in the starting line-up.
The Scots carved out the first real chance when Bannan's corner was nodded across goal by Phil Bardsley and fell for Christophe Berra at the back post only for the defender to rifle high and wide from close range.
The home side continued to push forward in search of the opener and Goodwillie's short pass was collected by Cowie but he was just off target with a well-struck shot.
Bannan then tried his luck from distance but his effort dipped well over the crossbar and never really troubled Zydrunas Karcemarskas in the Lithuania goal.
The Aston Villa midfielder attempted to turn provider with a long ball into the path of Naismith but his diving header was gathered by the goalkeeper.
Scotland looked more likely to open the scoring than their visitors and Fletcher tested Karcemarskas with a stinging shot at his near post, before Naismith nodded just over from the resulting corner kick.
Scotland should have opened the scoring a minute before half-time when Tadas Labukas handled Bannan's free-kick in the box and referee Kristinn Jakobsson pointed to the spot before brandishing a yellow card.
Fletcher stepped up for the spot-kick but Karcemarskas guessed correctly and dived to his left to block and prevent the home side from heading into the interval with the advantage.
However, Scotland went some way to making amends when they opened the scoring just four minutes after the restart.
Goodwillie's pass picked out the impressive Bannan and he delivered a cross from the right for Naismith who connected with a half-volley which smacked off the inside of the post and and into the back of the net.
Lithuania had the chance to apply some pressure when they were handed a free-kick 25 yards out after Berra was judged to have handled but Ramunas Radavicius' effort failed to make it past the wall as Scotland held firm.
At the other end, the referee could have awarded another penalty when Deividas Cesnauskis appeared to handle a Goodwillie cross before Naismith had the chance to connect with the header.
The Rangers midfielder then nodded over from six yards moments later as another opportunity was squandered, before hooking over the crossbar in the final minutes of the game.
Scotland managed to hold on for the win ahead of next month's double-header against Liechtenstein and Spain, which will determine their fate in Group I.