Authorities have since cancelled the Amber Alert that was issued for the girls.
Police said 6-year-old Dania Perez and 8-year-old Janeth Perez were taken by their father, 23-year-old Hostin Perez-Corza.
At a news conference on Friday, police said it all began when the mother of the girls went to a home in the 500 block of Chestnut Street to get the children.
Once she got there, police say Perez-Corza put a gun to her and led her into the house, holding her there.
Eventually the woman escaped, went to a friend's house, and called 911.
Police searched the home on Chestnut Street and discovered Perez-Corza, and the children, were no longer there.
Authorities issued an Amber Alert, including a description of the suspect vehicle.
Police say they issued an Amber Alert because they were worried about the safety of the children, considering the suspect's actions against their mother.
Then, around 8:45 a.m. Friday, a break came in the case when a police officer was driving through the Quality Inn and Suites in Bern Township, north of Reading.
That's when the officer was approached by a person who saw a vehicle matching the description in the Amber Alert.
Police soon determined that it was the vehicle they were looking for.
Officers arrived on the scene and started planning how they would take the suspect into custody, while also keeping the children safe.
However, while police were planning the operation, they say the suspect tried to check out of the hotel.
Police went to arrest him and a struggle ensued, leaving one officer with an injury to the hand.
Perez-Corza was eventually detained after being hit by a police stun gun.
The girls were found to be okay and are now safe.