"Chakvetadze had asked not to include her in the team," Russian tennis chief Shamil Tarpishchev said Monday.
Safina, at ninth a place below Chakvetadze in the rankings, would have missed the August Olympics despite her fine showing in Paris earlier this month because of the strength among Russian women.
But Chakvetadze has struggled for form this season following an armed robbery at her Moscow house late last year.
She escaped unharmed but later admitted she was still suffering mental stress from the ordeal. Her father, Jamal, a wealthy Russian bussinessman, was badly beaten up.
She lost in the second round at the French Open.
"Anna has no plans to compete in Beijing because her current form is far from ideal," Chakvetadze's mother was quoted as saying by the Allsport news agency.
The men's team will be picked according to the players' rankings, Tarpishchev said, meaning world No. 4 Nikolay Davydenko, No. 17 Mikhail Youzhny, No. 33 Dmitry Tursunov and No. 37 Igor Andreev will play singles in Beijing.