Iran striker Karim Ansarifard broke the deadlock in the 88th minute, which secured victory for his team.
The friendly was held at the 45,000-seat Otkritie Arena, the home stadium of Spartak Moscow.
READ MORE: Iran Head Coach: Russia-Based Players ‘Huge Help' for FIFA World Cup Team
The World Cup will get underway on June 14, with the matches set to take place in 11 cities across Russia.
Iran has been drawn in Group B along with 2010 World Cup winners Spain, reigning European champions Portugal and Morocco. Lithuania failed to qualify.