England's Test and one-day international number three was hit on the right hand by a short ball from Dale Steyn in Sunday's victory over South Africa at Lord's.
An X-ray on Monday suggested "no major fracture", but a subsequent MRI revealed he has broken a bone near the knuckle between his third finger and the back of his hand.
Trott will not need surgery but will miss the remainder of the domestic campaign, which concludes with Warwickshire's appearance in the Lord's final against Hampshire on September 15.
An England and Wales Cricket Board statement read: "Jonathan Trott has been ruled out of the remainder of the domestic season with an undisplaced fracture of the third metacarpal in his right hand.
"Although initial x-rays were clear, a subsequent MRI scan revealed a fracture at the base of his third metacarpal.
"No intervention is required, and the 31-year-old should be able to resume batting in three to four weeks and is expected to available for the tour of India next month."