City's Bernardo Silva and Mateo Kovacic both misfired in the shootout to put Madrid in the driving seat
Mutko told Reuters that authorities were working seriously on curbing racism in Russian football and that stadium security had been increased in the run-up to the tournament.
Russia will host the World Cup from June 14 to July 15 in 12 venues spread across 11 cities including Moscow, St Petersburg and Sochi.