The draw was enough to confirm progression to the knockout stages for Kurban Berdyev's side but Wigan could still threaten their bid to be group winners.
Bebras Natcho struck just before half-time to give the hosts the lead and put them on course to move on to an unassailable 13 points.
But, despite keeping their unbeaten European run intact, Rubin were pegged back just three minutes from full-time as Dejan Mezga slotted home.
Roman Eremenko came close to opening the scoring for the hosts inside the opening 10 minutes as he forced Maribor goalkeeper Jasmin Handanovic in to a smart close-range save.
Dmitri Tobinsky and Eremenko both missed decent chances as Rubin looked to make their early dominance pay but were almost caught out when Maribor's Slovenian midfielder Zeljko Filipovic fired over when well-placed inside the penalty area.
Natcho deservedly notched two minutes before half-time as the Israel international struck with a right-footed shot from just outside Handanovic's penalty area.
The second half proved to be a much closer affair as the visitors, who sit bottom of the group, looked to take something from the game.
Soares Arghus came close to levelling shortly after the interval but fired over from 20 yards with Matic Crnic and Ales Mertelj also registering good efforts.
The home side still threatened as Jose Salomon Rondon came close twice inside 60 seconds and Natcho forced a good save out of Handanovic with five minutes remaining.
But it was Mezga who was equalised shortly afterwards as he latched on to Crnic's late corner to finish smartly and secure a positive result for Ante Simundza's side, who retain a slim hope of being able to progress to the knockout stages.