Pavel Dmitrichenko – the alleged mastermind of the attack – was detained on Tuesday with Yuri Zarutsky, suspected of carrying it out.
A man accused of driving a getaway vehicle is also being held.
Sergei Filin’s eyesight was badly damaged when a masked attacker threw sulphuric acid in his face in January.
After a series of operations on his eyes, Sergei Filin has been moved to Germany, where doctors have expressed hope that months of further treatment may be able to restore good vision.
Sergei Filin, 42, also suffered facial disfigurement during the January 17 attack, outside his Moscow home.
It opened a window into bitter infighting and rivalries inside the Bolshoi theatre, shocking Russians, correspondents say.
Pavel Dmitrichenko’s flat was searched by Moscow police on Tuesday before all three suspects were confirmed as being detained. They have been held overnight.
“At the current time all three have signed confessions and have been placed under arrest,” Moscow police said on Wednesday.
“The necessary investigative work is being undertaken to establish all the circumstances of the crime.”
Confessions are common in Russia, though often the accused later complain of mistreatment.
Pavel Dmitrichenko, who has been with the troupe since 2002, is not one of the half-dozen very senior male dancers at the company, known as premiers, but he is a leading soloist one level down.
He has been performing the lead role in Sergei Prokofiev’s Ivan The Terrible.
It is unclear whether Yuri Zarutsky or the alleged driver, named as Andrei Lipatov, have any connection to the Bolshoi.
Police have questioned several Bolshoi employees as potential witnesses.
They are treating the attack as a premeditated act of grievous bodily harm, motivated by Sergei Filin’s professional activities.
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