The women have said the performance was meant as criticism of close ties between Putin and the Russian Orthodox Church and the clear if informal support its leader, Patriarch Kirill, gave Putin during his successful election campaign.
Western governments and rights groups have said the government's reaction to the "punk prayer" was excessive and are watching the trial closely. The judge is to give a verdict on August 17.
Rogozin, who some analysts view as a potential presidential candidate in the next election in 2018, did not mention Madonna by name in the English tweet on Friday or a Russian one on Wednesday.
But few Internet users had any doubt that he was referring to Madonna, who also spoke out in support of gay rights at a concert in St. Petersburg, Putin's home town, on Thursday night.
"She spoke about freedom, it is the state bureaucrats who are lecturing us every day on all the state channels," a Twitter user called Alexander Oleinik wrote in response to Rogozin's posting in Russian.
"Either take off the cross or put on your panties," Rogozin replied. His spokeswoman confirmed the messages were genuine.
Rogozin, former leader of the nationalist political party Rodina (Motherland), also wrote ironic messages about Pussy Riot, likening their supporters to a religious sect.
Rogozin was appointed deputy prime minister late last year as part of then prime minister Putin's drive to appeal to moderate nationalists.