The match was held at the Ta' Qali national stadium in Malta late Wednesday.
Russia's goals were scored by forward Artem Dzyuba (23rd minute), defender Mario Fernandes (35th minute), and another forward, Aleksandr Sobolev (90th minute), while Malta's lone goal was netted by forward Joseph Mbong (56th minute).
Russia and Malta are part of Group H of the qualifying tournament, along with Croatia, Slovenia, Slovakia, and Cyprus.