The two prisoners, identified as Raju Ninama and Subur Damor, were undergoing treatment in the prisoners' ward of the city's Sir Sayajirao General Hospital after being brought there from the Vadodara Central Jail.
They escaped by breaking the grill of a window in the ward between 2 AM and 5.30 AM today, police said.
Ninama was convicted in a rape case, while Damor was found guilty in a charge of attempt to murder.
Both of them belong to Garbada town in Gujarat's Dahod district.