Maximo Baez, the criminal investigations director, said one suspect confessed that he and four others planned to rob Perez's home. Police said they have identified the two other suspects, who remain fugitives.
Police said they expect to file charges later Saturday.
Perez, 55, last played in the major leagues for the New York Yankees in 1991. He was discovered by his ex-wife Thursday with severe head wounds in a town west of the capital of Santo Domingo. Police said he had been hit repeatedly with a hammer.
Police said one of the suspects knew Perez and told authorities that they sought to steal his $2,400 monthly pension for his 11-year career in the majors.
Another suspect was identified by police as a low-level drug dealer, while a third suspect was arrested Saturday after police said he sold one of Perez's cellphones for $6.25.
Perez, who had a rocky career including two suspensions for drug use, lived alone in San Gregorio de Nigua.
Perez compiled a lifetime record of 67-68 with the Atlanta, Pittsburgh, Montreal and Yankees.
The right-hander was first signed by the Pirates in January 1976 as an amateur free agent. He pitched for the Braves from 1982-85. He was 15-8 in 1983 and 14-8 in 1984.
In March 1992, he was suspended after failing a drug test the day he arrived for spring training with the Yankees. He was entering the final season of a three-year, $5.7 million contract, but never returned to the majors.