The raid occurred Monday after 40 gang-member inmates in the Stage II facility outside Guatemala City rioted a day earlier, killing two guards and grabbing the four hostages, who were badly wounded.
One of the captives died shortly after the raid; the second died Tuesday, the hospital treating them said in a statement.
Of the two surviving guards, one is in a critical condition and the other was stable.
The outbreak of violence in the juvenile center occurred less than two weeks after 40 teenage girls died in a fire at a nearby overcrowded youth shelter in the same town of San Jose de Pinula.
In both cases, those being held had protested mistreatment at the hands of guards. In the youth shelter, girls had complained of sexual abuse.
The deadly incidents have piled pressure on President Jimmy Morales and his government, with protests and public anger boiling over.
The head and senior officials of the social welfare ministry responsible for both facilities were sacked and arrested on charges of manslaughter after the girls' fire deaths.
Following the raid on the Stage II detention center, police reported stepped-up attacks on officers across Guatemala by the Barrio 18 gang to which the inmates belonged. Two uniformed officers were killed and nine wounded.
A police spokesman, Pablo Castillo, said the motive of the attacks was not known, but have not ruled out that they might be in reprisal for the raid.
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