The three wore revealing, brightly colored clothing and covered their faces with balaclava-style masks in a style "inappropriate" for a church before making use of a microphone and electric guitar, the court was told.
Video footage of the "punk prayer" protest song was placed online, although the judge said it was not clear who had posted it.
Sirovaya said that the apologies by the defendants "were not sincere" and described their conduct as "an unprecedented act of hooliganism by women."
Evidence from character witnesses for the three women was also read out. Alyokhina was described as being a writer of poetry, a vegan and a good mother, RIA Novosti said.
Pop star Madonna last week performed Pussy Riot-style in a face mask and with the group's name on her back during a packed Moscow gig. She's one of a number of celebrities to back the women's cause.
"Everyone has the right to free speech, everywhere in the world. Maria, Katya, Nadia, I pray for you," Madonna said at Tuesday's concert, according to RIA Novosti. "They did something brave with their action. And I am praying for their freedom."
Rallies in support of Pussy Riot were also organized Friday outside Russian embassies around the world, including in London and Washington.
Putin criticized the women's action this month but said they should not be judged "too harshly," RIA Novosti said. He added that he hoped the court makes "the right decision."
Pussy Riot specializes in sudden, often illegal public performances, including one in Moscow's Red Square.
The "punk prayer" was inspired by the women's anger about the relationship between the Russian government and the Orthodox Church, according to the band's manager, who is married to one of the women.
The Orthodox leader Patriarch Kyril has been widely reported as saying Putin's years in power have been a miracle from God.
Putin won reelection to the presidency in March in a vote that international observers said did not meet international standards.
The presidential election came just months after allegations of fraud in parliamentary elections prompted the largest anti-government demonstrations Russia had seen in two decades.