Emenike, the club's top scorer this season, aggravated a back injury in Saturday's league game in Samara.
The Nigerian, who scored both of Spartak goals in last month's 3-2 defeat by Celtic, also missed the team's 2-1 win over Benfica two weeks ago with the same problem.
Brazilian Welliton, who topped the Russian scoring charts in 2009 and 2010, is sidelined with an unspecified problem, a Spartak spokesman said.
The Muscovites already have several key players out with injury in addition to Emenike and Welliton, including first and second-choice goalkeepers Andriy Dykan and Sergei Pesyakov.
Captain Sergei Parshivlyuk, Brazil midfielder Romulo and Ireland winger Aiden McGeady are also injured.
Spartak's third-choice keeper Artem Rebrov was in goal for the first Benfica match in Moscow.
Barcelona top the standings on nine points, ahead of Celtic (four), Spartak (three) and Benfica (one).