The Spanish champions, with Lionel Messi on the bench, wasted a host of chances in the first half, with striker Pedro the main culprit against the team who took four points off Barcelona in last season's competition.
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Pedro missed a golden early opportunity, hitting a crossbar with the goal at his mercy following a perfect pass by David Villa. Pedro had another chance late in the first half but again shot wide of the post from 12 metres.
The Russian champions converted their first real chance, captain Christian Noboa scoring from the spot after Barca defender Dani Alves brought down Vitaly Kaleshin in the 30th minute.
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Thirty minutes later Spain striker Villa equalised with another penalty after Andres Iniesta was fouled inside the box.
However, Rubin, who stunned the then European champions 2-1 in the Nou Camp before holding them to a 0-0 home draw in the group stage last season, frustrated the Catalans again with their defensive approach.
CHANCES WASTED
"It was very difficult for us to score tonight as Rubin had many players guarding their goal," Villa told reporters.
"Still, we had a lot of chances, hit a post and also their keeper played well when he had to."
Barca coach Pep Guardiola introduced Messi shortly after scoring the equaliser, looking to break down the home team's fortress.
The World Player of the Year, who netted twice in Barca's 5-1 demolition of Panathinaikos in their opening group game, had one good chance but Rubin keeper Sergei Ryzhikov did well to avert the danger.
At the other end, Rubin substitute Obafemi Martins could have given the hosts an unlikely victory three minutes from time but the Nigerian striker hit the post from close range.
After Martins had wasted his chance, Iniesta could have snatched the three points for the visitors with virtually the last kick of the game but he just clipped a shot over the bar.
Rubin earned their first point in the competition following a surprise 1-0 defeat at Copenhagen in their opening fixture and Barcelona have four points after two games.
"We needed at least a point to keep alive our chances in the group after losing in Copenhagen so I must admit that we're satisfied with the draw," Rubin coach Kurban Berdyev said.
Greek side Panathinaikos were hosting Danish champions Copenhagen in the other Group D match later on Wednesday.
