The host nation appeared set to endure death by a thousand cuts against La Roja, who passed the ball over 1,000 times in their last 16 encounter.
A first-half own goal from Sergei Ignashevich gave Spain the lead, but an Artem Dzyuba penalty, awarded after a strange Gerard Pique handball, gave Russia a route back into the game.
Spain, who won the competition in 2010, then dominated possession, but were unable to break the hosts' stubborn defence down, and missed two penalties in the shootout, with Koke and Iago Aspas both seeing their efforts saved. Russia, by comparison, scored all four of their efforts.
And Samedov was proud of the way he and his team-mates executed their gameplan.
"On the whole, it was a fantastic game and result, as we showed our dedication and executed the match plan," Samedov told reporters.
"We are certainly very proud to enjoy the victory over the 2010 world champions and this is a very fantastic result.
"The Spanish squad is a very outstanding team, which play in a total control of the ball.
"We needed a lot of patience and had to execute all of our rough work, but it was the only antidote against such team."