The Russian champions beat Barca at the Nou Camp last year and went ahead when Cristian Noboa scored a 30th-minute penalty.
Villa spared Barca's blushed with his spot kick on the hour, although Rubin almost snatch a late winner when Obafemi Martins hit the post with a header.
"I'm happy with the performance of the players," coach Pep Guardiola told Barca's official website. "We had enough chances to win the game."
He also said of the introduction of Lionel Messi in the second-half, "he will try to continue making progress in his recovery. We are happy that he has returned."