The home side won the day thanks to a late Romand Shirokov goal.
Fernando Santos rested Cristiano Ronaldo, João Moutinho and André Gomes whilst giving Gonçalo Guedes his senior debut. Nélson Oliveira returned to the starting line-up for the first time since 2013 and André André earned only his third cap.
As early as the eighth minute, the Zenit St. Petersburg striker Artem Dzyuba latched onto a long cross but Pepe cut in front of his shot to clear the ball away for a corner.
The dangerous Dzyuba then struck the crossbar with a towering header after Samedov picked him out from the right wing. Rui Patrício got down well to smother a Roman Shirokov effort when the Spartak Moscow striker picked up Pavel Mamayev’s through ball.
It was one-way traffic as Portugal struggled to gain a foothold. Gonçalo Guedes did have an excellent chance to open his international goal account after good work by Nelson Oliveira but the Benfica youngster hit his fierce shot straight at the Russian keeper.
Russia came storming back on the counter just before the interval. Samedov should have done better after being teed up by Dzyuba, but the Lokomotiv Moscow winger blasted his effort over the crossbar.
In the second-half, Russia continued to dominate although Cédric nearly found Nelson Oliveira with a cross from the right wing in the seventieth minute. FC Porto’s Ruben Néves then earned his first cap, coming on for André André.
The youngster picked out Nani with a fine cross immediately after coming on but the former Manchester United player headed straight at Akinfeev.
Ricardo Pereira became the third player to make his first appearance for Portugal on the night in the 83rd minute in place of Gonçalo Guedes.
João Mário nearly found a winner four minutes from time with a shot from a tight angle which Akinfeev did well to push wide. But it was Russia that claimed a deserved victory in the 89th minute after a slick passing movement down the left.
Denisov played in Fedor Smolov through the left channel, and his cross was well controlled by Dzyuba for Shirokov to strike past a helpless Rui Patrício.
Portugal again lacked a cutting edge without Ronaldo, but also struggled mightily in possession without the experience of Moutinho and Tiago. Four senior debuts were made, and Santos clearly understands the need to identify new goal-scorers as evidenced by the inclusion of Lucas João, Oliveira and Gonçalo Guedes.