Ibragimov kept his WBO title with a unanimous decision over Holyfield, who turns 45 next week and was trying to become the second-oldest heavyweight champion.
Fighting before a home crowd, Ibragimov improved his record to 22 wins and one draw with a slick, counter-punching display. Holyfield dropped to 42-9 with two draws.
The crowd at Khodynka Arena chanted "Sultan! Sultan!" at the end of the bout, with both fighters embracing at the final bell.
The judges scored the 12-round fight 118-110, 117-111 and 117-111.
Ibragimov, a 32-year-old Russian, will now try and unify a fractured division. The other heavyweight titles are held by Wladimir Klitschko (IBF), Ruslan Chagaev (WBA) and recently declared champion Samuel Peter (WBC).
George Foreman became the oldest heavyweight champ at 45 and 300 days when he knocked out Michael Moorer to win the WBA and IBF titles in 1994.
This was Holyfield's 23rd title bout in a 20-year heavyweight career. In title fights, he beat James "Buster" Douglas (IBF, WBA and WBC) in 1990, Mike Tyson (WBA) in 1996, Michael Moorer (IBF) in 1997 and John Ruiz (WBA) in 2000.
Holyfield needed a knockout as the last round started. But on the odd occasion he trapped Ibragimov on the ropes to throw left and right hooks, the Russian would tie him up in a clinch and force the referee to intervene.
The fight began with both fighters feeling each other out, although Holyfield looked happy to tie up Ibragimov to negate his superior hand speed. It also appeared Holyfield accidentally butted Ibragimov's nose.
In the next round. Holyfield rocked Ibragimov with a heavy right and caught him with a glancing left hook. The two fighters exchanged stares and words at the bell.
Ibragimov's snaking jab allowed him to circle the ring and fight on the outside, forcing Holyfield to rush and try to get closer. But that only meant his well-regarded chin took a couple of straight lefts.
Ibragimov's faster hands and feet kept him ahead on the scorecards.