Moscow's Basmanny Court ruled that Akram Azimov was to remain in custody until June 3, agencies reported.
Russia's FSB security service said the younger brother Abror Azimov, born in 1990, was "one of the organisers" of the attack that killed 14 people.
The FSB said on Wednesday that Akram Azimov, who was born in 1988, "helped transport money used to prepare for the attack, as well as arranging contact with emissaries of international terrorist organisations."
Abror Azimov, who is also being held in custody as the investigation continues, denied he had helped mastermind the attack in a court appearance this week.
Russia's FSB security service said on Thursday that it was close to identifying those who ordered the bombing.
FSB head Alexander Bortnikov told reporters that this had been "practically established," Russian news agencies reported.
It was not immediately clear if Bortnikov was referring to a group or an individual.
Authorities have attributed the attack to 22-year-old Akbarjon Djalilov, thought to be a Russian national born in Kyrgyzstan, who died in the blast.
There has been no claim of responsibility but investigators say they are examining possible links to Islamic State jihadists.
Eight other people - all from mainly Muslim Central Asian countries - have also been detained in Moscow and Saint Petersburg over alleged involvement in the attack.