Dmitry Rogozin said earlier Friday that he would resign from his post but remain a party member.
"I ... will also ask my colleagues in the party to support the candidacy of my best friend and like-minded person Alexander Babakov for leadership in the party," he said.
Babakov is chairman of the party's presidium and Rodina's top sponsor.
Leaders of the center-left nationalist bloc Rodina said last week they would push for the party to abandon nationalist and xenophobic ideology.
Rodina was banned from participating in December 4 elections to the Moscow legislature after the ultra-nationalist Liberal Democratic Party of Russia (LDPR) filed a suit with the Moscow city court alleging a Rodina television commercial incited inter-ethnic tension.
The commercial featured three dark-skinned men from the Caucasus tossing a watermelon rind at the feet of a passing Slavic girl pushing a stroller. A voice-over against the background of the Rodina emblem urged people to "remove the rubbish from Moscow."
