The Russian champions had survived Maribor's lively start to the game when a firework projected from the Spartak fans travelled more than half the length of the pitch and landed not far from referee Deniz Aytekin's feet.
Should the club be disciplined it will further compound their disappointment after Damjan Bohar's late equaliser denied them a winning return to the Champions League group stage after a five-year absence.
Second-half substitute Aleksandr Samedov gave Spartak the lead just before the hour mark as smoke continued to billow from the area in which the visiting supporters were seated, but Bohar levelled the game with a fine finish in the 85th minute to spark wild celebrations from the home crowd.
Maribor will be hard pressed to take points from their remaining five Group E games - with matches against Liverpool and Sevilla to come - but coach Darko Milanic saw his charges put in a spirited performance that might have yielded more than just a point had they taken their chances.
Martin Milec drew an early save from Artyom Rebrov in the Spartak goal when he cut inside from the right flank in the first minute and struck a bouncing shot that the goalkeeper could only parry away.
Play swung from end to end in the game's early stages and Andrey Eshchenko blazed a shot over the crossbar after a dangerous run by Quincy Promes, but the home side were in the mood to attack and Valon Ahmedi let fly from 25 yards after 10 minutes, forcing another good save from Rebrov.
Spartak's quality began to show after 25 minutes when a flowing passing move saw Mario Pasalic freed Promes, whose flick put Eshchenko one-on-one with Jasmin Handanovic, but the winger lofted his shot high of the target.
Promes is Spartak's top goal-scorer this season and he almost added another to his tally with a dipping drive from 20 yards that flew just wide on the half hour mark, as Maribor ended the first half with little of the energy and verve they had shown early on.
Spartak brought on Samedov at half-time and four minutes into the second half he danced into the penalty before chipping a shot narrowly over the crossbar.
His introduction proved decisive 10 minutes later when he latched onto the rebound after Handanovic saved Fernando's shot and rifled the ball high into the net, prompting explosive celebrations from the Spartak supporters.
Bohar almost equalised immediately with a close-range header that Rebrov saved at full stretch, and Maribor full-back Mitja Viler sent an angled drive whistling past the post after 68 minutes as the hosts pushed hard to salvage a point.
Fernando should have made it 2-0 when Luiz Adriano teed him up for a one-on-one with Handanovic, but the Brazilian midfielder dragged his shot wide. Promes tried his luck with an audacious free-kick from 30 yards, but Handanovic rose well to save.
But Maribor never gave up and with five minutes left they were rewarded when Martin Kramaric played the ball out to Bohar on the left side of the Spartak penalty area and the midfielder unleashed an unstoppable drive into the far corner of the net to earn his side a precious point.