But substitute Nejc Pecnik grabbed what could prove a crucial away goal for Slovenia ahead of the return leg in Maribor on Wednesday when he scored against the run of play with three minutes remaining.
Bilyaletdinov had put the home team ahead in the 40th minute when he took a pass from Roman Pavlyuchenko just inside the penalty box, turned neatly past Slovenia defender Marko Suler and fired a right-footed shot into the top corner.
The Everton winger doubled the lead seven minutes into the second half, beating Slovenia keeper Samir Handanovic from close range with his second attempt following good work by captain Andrei Arshavin.
The Russians are seeking their 10th World Cup appearance, including the days of the Soviet Union. Slovenia's only previous showing at soccer's greatest spectacle came in 2002.
Despite a late letdown, Russia coach Guus Hiddink, who has never failed to guide his teams to a major tournament, remained confident of clinching a place in next year's finals.
"We had a good chance to put the result beyond doubt in the first leg," the Dutchman, who is seeking to steer his fourth team to the World Cup, told a news conference.
"We had a two-goal lead and chances to add a couple more but gave up a late goal, but I think we're quite capable of winning in Maribor and securing a ticket to South Africa."
SLOVENIA FIGHTBACK
His Slovenian counterpart Matjaz Kek was disappointed with the outcome.
"Sure, I'm not happy, but 2-1 is still better than 2-0," he said. "But we never gave up, we fought until the end and it gives us a chance in the return leg."
After a nervous opening Russia took control of the match played on artificial turf.
Yuri Zhirkov had the first clear chance for the home side following a great solo run through the Slovenian defence but his low shot was blocked by Handanovic.
Sergei Ignashevich later tested the tall goalkeeper twice from long-range free kicks and Handanovic also made a fine save from Pavlyuchenko's diving header in the second half.
The Russians, cheered on by a near capacity 80,000-strong home crowd at Luzhniki stadium, piled on the pressure in the second half, coming close on several occasions.
Arshavin, one of the most active players on the pitch, could have added a third and Bilyaletdinov just missed a chance for a hat-trick late in the game.
But Slovenia had the last word when Pecnik, on the pitch for just five minutes, was left unmarked at the far post and headed into an empty goal following a save by Russia keeper Igor Akinfeyev.
