Going into the match needing a win and the Lille-Trabzonspor match to end in a draw in order to qualify, the defender headed home with four minutes to go, seconds after Diego Milito had headed against the crossbar at the other end.
The Russian side took the lead five minutes after the break through Ivorian striker Seydou Doumbia, but dreams of progression appeared to have evaporated when Argentine midfielder Esteban Cambiasso equalised within a minute.
With Lille-Trabzonspor ending goalless, CSKA qualified in second place with eight points from six games, two points behind 2010 winners Inter. Trabzonspor go into the Europa League having finished third with French champions Lille bottom.
CSKA's leading scorer Doumbia said it was a magical night.
"It was unbelievable to score here," he told uefa.com. "I hadn't scored for two matches so it was a great relief. It was tough to take when they equalised but I was so happy when we scored again."
Inter coach Claudio Ranieri said he was happy with his side despite a second home defeat in five days after Saturday's league reversal against Udinese, which left them 15th in Serie A.
"It seems strange but the boys are doing well," he told Sky Sport channel.
"When you go home with a defeat it's not great, but now we have to pick ourselves up for Saturday's match against Fiorentina [at home]."
POURED FORWARD
CSKA enjoyed a bright start but it was the home side who should have taken the lead on 10 minutes when a three-man break ended with a brave Vladimir Gabulov diving to cut out Diego Milito's weak cross.
With the frantic early pace resembling the end rather than the start of a match, the Russian side's defences were breached a second time two minutes later when Milito fed Yuto Nagatomo but Gabulov was again on hand to save the Japanese defender's sidefoot finish.
Inter goalkeeper Luca Castellazzi was called into action for the first time on 28 minutes, throwing himself to his left to parry Vagner Love's curling strike from distance as the visitors continued to press but with more caution.
Love squandered a glorious chance to give CSKA the lead 10 minutes before half-time when he climbed superbly inside the six-metre box to meet a free kick but managed to head over the bar with the goal gaping.
On the stroke of half-time, Milito twice went close to breaking the deadlock, firing a fraction over with a fizzing effort from the edge of the box seconds after shooting against Gabulov's frame from another well-timed break.
With the news that Lille and Trabzonspor were still drawing at half-time, CSKA poured forward at the start of the second half and they were rewarded within five minutes when Love slipped in the onrushing Doumbia to finish coolly past Castellazzi.
Russian celebrations were short lived however as Inter equalised in the very next attack when Cambiasso was on hand to poke home with the outside of his left foot after Gabulov had parried a powerful
