The visitors seemed to have won the tie with only minutes to spare through Salomon Rondon, but the Japan international struck at the death to deny the Venezuelan and his team
The Russians took the lead through Aleksandr Ryazantsev indirectly from the penalty spot inside the first 17 minutes, before Marko Livaja, on his full Nerazzurri debut, restored parity shortly before half-time.
Salomon Rondon seemed to have stolen all three points with a fine finish in the latter stages, but it was not to be as the Japanese defender volleyed home in the second minute of stoppage time.
An absorbing clash was witnessed at the Giuseppe Meazza, with both teams keen to get their European campaigns on the road, and it was Inter who began most positively, with Antonio Cassano especially lively from the off.
However, arguably against the run of play, Rubin were presented with the chance to strike first blood - Jonathan fouled Karadeniz Gokdeniz in the area, and although Bibras Natcho saw his penalty well stopped by Samir Handanovic, Ryazantsev applied the rebound.
The hosts were then gifted a pair of decent chances to redeem themselves, but Jonathan could not place his shot past Sergey Ryzhikov from several yards out, while Livaja failed to make a glorious chance count off his head.
Still, they continued to chip away at the Rubin resistance, and they were good value for their respite, as Cassano's through pass was read by Esteban Cambiasso, who curled in a ball for ex-Primavera prospect Livaja to nod in.
A similar story unfolded after the break, as Inter continued to rifle in shots at will, but without any luck. Philippe Coutinho and Fredy Guarin being most guilty of speculative drives. It appeared the Italian giants had begun to run out of ideas.
It allowed Rubin to regain control of the tie, and they seemed to have found the winner with only four minutes to spare. Salomon Rondon was released in the clear by Roman Eremenko, before overcoming Andrea Ranocchia and coolly tucking a finish away.
But Yuto Nagatomo had other ideas. The likes of Diego Milito and Alvaro Pereira were hauled on as the Milanese side went to look for the all-important second goal, and the Argentine's cross was struck with aplomb by the full-back.
The result means all the sides in Group H are level on a single point, as Partizan Belgrade and Neftchi Baku also registered opening-day draws. Next up for Inter is a home match against Siena in Serie A.