Fedor Cernych had sent the visitors ahead just before the hour in Glasgow, but McArthur nodded home from close range in the latter stages as the points were shared in the Group F clash.
Scotland had a half-chance inside three minutes when Grant Hanley met a deep cross at the far post, but the defender's header was always dropping wide as Lithuania survived a dangerous early moment.
Chris Martin also came close for Gordon Strachan's side in the first period, but it was a very frustrating opening half for the hosts, who were booed off by some sections of the crowd at the interval.
Scotland came out swinging in the second period as Andrew Robertson started to cause problems in a wide position and the full-back set up Robert Snodgrass, who had a goal-bound strike blocked, before Martin headed just wide in the 54th minute.
It was the visitors that took the lead just before the hour, however, when Vykintas Slivka slipped a pass in to Cernych and the number 22 found the bottom corner with a powerful finish.
James Forrest struck wide of the post as Scotland looked for an immediate response, but the hosts trailed entering the final 20 minutes as Lithuania held firm at Hampden Park.
The pressure was relentless though as Strachan's side, who will travel to Slovakia on Tuesday night, looked to avoid a damaging defeat and McArthur's close-range header after a Hanley flick ensured that the hosts would claim a point.