Spain controlled the game as expected but struggled to create genuine chances, with Akinfeev sharp on the few occasions they did before saving from Koke and Iago Aspas to seal a 4-3 win on penalties.
Spain were gifted the lead through Sergey Ignashevich's early own goal, then themselves handed Russian Federation an equaliser via Gerard Pique.
Mighty Spain dominated the field at Luzhniki Stadium, dulled the senses with mind-numbing ball movement around the perimeter of the penalty area Sunday.
Gerard Pique handled Artem Dzyuba's header and the Zenit St Petersburg forward sent David de Gea the wrong way for his third goal of the tournament.
Artem Dzyuba - 7 - Imperious in the air, the mountainous forward caused a number of problems for the Spain back-line, and ultimately played the key role in winning Russian Federation a first-half penalty and converting it. The old days of tiki-taka's preeminence delivered a performance in which the first shot on target from a Spanish player - Sergey Ignashevich's 11th-minute own goal came off the back of his leg - came on 45 minutes.
Meanwhile, Mark Geiger has been assigned to referee Tuesday's World Cup last-16 match between England and Colombia, four years after he became the first American to officiate in the knockout stage of soccer's showcase.
Russia fans react after Russia won the penalty shoot-out during the Russia 2018 World Cup round of 16 football match between Spain and Russia at the World Cup.
Andersson's Swede delight but Mexico miss golden chance
When Edson Alvarez got his legs tangled and turned the ball into his own net, the writing was on the wall for Mexico . Once again the players have been highlighting the importance and value of the strong unity within the group.
Andres Iniesta, the elegant midfielder who was a symbol of Spain's golden generation, retired from global soccer following the team's loss to Russian Federation in a penalty shootout at the World Cup on Sunday.
A Russian fan celebrates his team's win over Spain in the World Cup.
Hosts must rebound quickly for last 16 clash, the 2010 champions who have slipped under the radar after a tumultuous start to the tournament.
"I think the manager chose the right tactics to do it by being very strong by the defensive point of view, by giving the initiative to Spain by being in control defensively, which they did", Mourinho said.
The Russia goalkeeper was again involved early in the second half, flying to his left to pluck a spinning Jordi Alba effort from the air. He also ensured the game needed 30 extra minutes with back-to-back diving saves in the 85th to deny substitutes Iniesta and Aspas.
Spain join Germany, Argentina and Portugal as the fancied teams eliminated.
"It's reality that today has been my last match for the national team", he told reporters. "We have to get better, we haven't produced our best football", said Bayern Munich midfielder Thiago Alcantara. Spain made their extra substitution seven minutes later when Rodrigo Moreno replaced Marco Asensio.