The defendants, Tova Noel and Michael Thomas, had been accused of falling asleep and surfing the internet rather than checking on Epstein every 30 minutes at the Metropolitan Correctional Center in downtown Manhattan.
Epstein, who had pleaded not guilty to sex trafficking charges, was found hanging in his cell on Aug. 10, 2019. New York City's medical examiner called the financier's death a suicide.
US District Judge Analisa Torres in Manhattan told Noel and Thomas their deferred prosecution agreement "offers you a chance to avoid a criminal conviction. I trust that you'll comply with the terms."
Noel and Thomas will serve six months of supervised release and complete 100 hours of community service, preferably related to criminal justice.
They must also cooperate with a probe by the US Department of Justice's inspector general, including the circumstances surrounding Epstein's death.
Both defendants admitted to having "willfully and knowingly" falsified records to make it seem they were checking on Epstein, who had been on suicide watch the previous month.
Prosecutors said Noel and Thomas actually shopped online, checked sports news, and appeared to nap for two hours each.
The probe began under then-Attorney General William Barr, who was angered that a high-profile inmate like Epstein was able to kill himself.
Management was overhauled at the Manhattan jail, which has experienced staff shortages and criticism for poor conditions.
Noel's lawyer Jason Foy and Thomas' lawyer Montell Figgins said their clients were happy the criminal case was resolved. They have suggested their clients were scapegoated for problems within the Federal Bureau of Prisons.
"This case should sound the alarm that the criminal justice system is in disrepair," Figgins said. "There are rampant problems in our nation's prison system that must be fixed."
Epstein's longtime associate, British socialite Ghislaine Maxwell, has pleaded not guilty to charges she procured four underage girls for him to sexually abuse, and is awaiting trial.
She has been denied bail three times and is being jailed in Brooklyn, where her lawyers said she is subjected to intrusive monitoring on a misplaced concern she might also kill herself.
The case is US v. Noel et al, US District Court, Southern District of New York, No. 19-cr-00830.