It was a night of frustration as the hosts failed to make the most of their chances.
Here Andy Newport takes a look at five things we learned from the match:
Scotland under pressure to bounce back
After getting their qualifying campaign off to the perfect start in Malta, Gordon Strachan’s men were desperate to build some early momentum against the Lithuanians.
But they never got going against Edgaras Jankauskas’ stuffy outfit and were hit with a sucker-punch when Lithuanian skipper Fedor Cernych slammed the visitors ahead.
James McArthur grabbed a late leveller but with Group F set to be a fiercely contest battle, Tuesday’s trip to Slovakia already appears vital to Scotland’s Russia 2018 hopes.
Strachan’s problem starter struggling to get up to speed
The big worry for Strachan pre-match was Grant Hanley’s lack of action this season.
The defender has played no more than a bit-part role since signing for Newcastle back in July but remains Strachan’s first-choice pick at the heart of defence.
However, it was glaringly apparent just how short on sharpness Hanley was as he was left chasing shadows when Cernych skipped past him with ease to net his side’s shock opener.
Scotland lack Scott Brown’s energy
Saturday’s match was the second since Celtic skipper Brown announced his international retirement.
The Parkhead midfielder is benefiting from the extra rest he is now getting after putting in some tremendous displays for Brendan Rodgers’ team but that is no consolation for Strachan, who could have done with his drive.
Darren Fletcher has taken over the captain’s armband but a thigh injury ended his 75th cap after just 45 minutes. McArthur showed he can be the man to provide Scotland with extra dynamism after capping an encouraging display with his goal.
Oliver Burke is a diamond who needs further polishing
The RB Leipzig winger must feel he is carrying the hopes of a nation on his shoulders given how much has been said and written about the 19-year-old since clinching his £13million move to Germany this summer.
The former Nottingham Forest youngster certainly did his best to drive Scotland on but there remains a rawness to his game. The Tartan Army would do well not to expect too much too soon.
Lithuania are world-class time-wasters
Jankauskas’ men might not make it to the World Cup but they proved they are among the best on the planet at running down the clock.
Time and again their men hit the deck claiming to be suffering from cramp.
Their antics obviously got to Strachan, who had an angry exchange with the visitors’ medics when they tried to use up another valuable few seconds by running to tend to another grounded opponent as time ran out for his men to find a winner.