Pichugin has insisted he is innocent.
He was originally sentenced last August for the killings, but prosecutors appealed against that ruling in an attempt to win the life sentence.
In Russia, a longer term replaces a shorter one.
Judge Pyotr Shtunder said as he read the verdict: "The court established that on January 21, 1998 Pichugin arranged the killing of Valentina Korneyeva, the director of commercial firm Feniks."
The judge also said Pichugin murdered the mayor of a Siberian oil town and the driver of an oil businessman as well as trying to kill two others.
Pichugin was convicted in 2005 and sentenced to 20 years for murdering a provincial businessman and his wife.
Supporters of Khodorkovsky, who himself is serving an eight-year term in a Siberian farm for fraud and tax evasion, say he is being punished by the Kremlin for his political ambitions along with other people connected to Yukos.