The second half was played at nearly walking pace, brought very little drama - ditto the first extra time of the tournament - and Fernando Hierro's side paid dearly for their lack of ideas and intensity by exiting 5-3 on penalties in the shootout.
They had taken the lead on 12 minutes after Sergei Ignashevich deflected a Marco Asensio free-kick into his own net.
A total of 32 national football teams entered the 2018 FIFA World Cup and only 16 of them proceeded to the knockout phase after the group stage, which kicked off on June 14 and ended on June 28.
Spain are yet to hit their groove and take on the hosts at the Luzhniki Stadium in Moscow for a place in the quarter-finals.
Russian Federation were largely expected to just make up the numbers at their own tournament after entering with a seven-match winless run and ranked the lowest of the 32 teams.
A deep corner was met by Dzyuba, whose header struck the outstretched arm of Pique, with referee Bjorn Kuipers contemplating his decision before pointing to the spot. The goal, slightly fortunate thought it was, was justification for Russia's reactive approach. "He told me that he will play in the match against Spain, if not in the starting line-up then as a substitute", TASS quoted Dzagoev's father Tarel as saying.
The following penalty shootout proved that that hosts Russian Federation was stronger scoring all five shots, while goalkeeper Igor Akenfeyev saved one of the strikes from Spain.
"Spain plays the same style as in previous years", said the 38-year-old defender.
The CSKA Moscow goalkeeper has been a regular for his national team since making his worldwide debut fourteen years ago and while the 32-year old has more clean sheets than any other Russian goalkeeper in history, his club record in European tournaments has been not quite up to the mark.
Yuri Zhirkov - 4 - A sluggish challenge on Nacho led to the opening goal for Spain, and the former Chelsea full-bak exhausted as the match went on before coming off at half-time. He guessed right. Advantage Russia. "We didn't play quite the way we wanted but it's hard when you don't have the ball and you spend that much time defending".
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