The result, with Slovenia captain Valter Birsa and Lithuania's Arvydas Novikovas each scoring from the spot, left the Slovenians third in the section on 13 points from nine games, three ahead of Estonia and Lithuania.
If all three sides are level on points after Monday's final round of games, Slovenia will finish highest with the best head-to-head record.
If Slovenia and Estonia finish tied on 13 points, the race will go down to overall goal difference in the group as both sides have beaten each other 1-0 at home.
Apart from being strong favourites to get a result away to San Marino, the Slovenians also have a vastly superior goal difference of plus five to Estonia's minus four in the group.
Estonia entertain Switzerland in their final match while Lithuania are at home to England.
The draw in Ljubljana's Stozice stadium also meant that the Swiss, 7-0 winners over San Marino, joined England, who beat Estonia 2-0, in next year's tournament in France.
Slovenia dominated the opening period and, having missed several chances, they took the lead on the stroke of halftime when Birsa converted a penalty.
Dutch referee Bjorn Kuipers awarded the spot kick after a vicious Jasmin Kurtic shot struck Marius Zaliukas on the arm and Birsa made no mistake, sending Emilijus Zubas the wrong way.
The Slovenians came close to doubling their advantage three times before some of the floodlights went out and seemingly turned around the two teams' fortunes.
Kuipers decided the match should continue and Lithuania capitalised after Slovenia defender Branko Ilic clumsily handled a teasing cross from the right in the closing stages.
Novikovas drilled the penalty into the top right corner and the Lithuanians then held off a fierce Slovenian onslaught in a frantic finish to claim a point.
(Writing by Zoran Milosavljevic in Belgrade; Editing by Ken Ferris)
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