Lokomotiv Moscow took the lead in the 17th minute through Manuel Fernandes.
Amkar Perm were back on level terms thanks to Samuel who converted a 48th minute penalty.
And in the 59th minute, Samuel scored what proved to be the winner to end Amkar Perm’s two league games without a win (one draw, one loss).
The game was Samuel’s third Russian Premier League appearance for Amkar Perm since joining them on loan from CSKA Moscow.
The win temporarily moved Amkar Perm out of the relegation zone to 12th on 25 points in the 16-team league table.
A win for Dinamo Moscow in 13th spot on 24 points against Arsenal Tula on Saturday will see Amkar Perm drop into the relegation play-off position.