The boys are 14 and 15 years old, according to Troy Harrison, PISD assistant police chief.
On Monday, the hamster was not acting naturally, Harrison said.
The hamster had a substance coming out of its eye sockets, Harrison added.
The teacher took the pet to a veterinarian who said that the animal had suffered trauma to the head. It is believed that the students thumped the hamster on the head, Harrison said.
The animal had to be euthanized. District police were contacted by the teacher on Wednesday, Harrison said.
He said the investigation was completed on Thursday.
The students admitted taking the hamster out of the cage and treating the hamster in a rough manner, Harrison said.
The Harris County District Attorney's Office accepted felony animal cruelty charges against the students, Harrison said.
If children are allowed to harm animals, they may be more likely to be violent later in life, according to information by the Humane Society at www.hsus.org.