England forward Bowen was substituted during the second half of Sunday's 5-0 thrashing.
"West Ham United can confirm Jarrod Bowen sustained a fractured foot injury in Sunday's Premier League fixture against Liverpool," a club statement read.
"The injury to his left foot, picked up in the first half at London Stadium, will sideline the Hammers captain heading into the New Year."
Bowen has been a key player for the Irons again this season, scoring six goals in all competitions.
The 28-year-old revealed he had sustained the injury during the first half, but tried to play on.
"Unfortunately in the first half of our game on Sunday I suffered a fracture to a bone in my foot," Bowen wrote on Instagram.
"As always I tried to fight on and continue playing until I physically couldn't.
"Injuries happen in football, but I'm already looking forward to getting back out there as soon as possible. See you all soon."
West Ham return to Premier League action at Manchester City on Saturday.
Irons forward Michail Antonio, meanwhile, has been discharged from hospital he continues his recovery following a car crash earlier in December.
The 34-year-old Jamaica international needed surgery on a lower limb fracture after being involved in a road traffic accident on December 7, and is expected to face a lengthy spell of rehabilitation.