He was being held Saturday night in the county jail in lieu of $250,000 bond.
Rodriguez, 47, is charged in the shooting death of Israel Borrego, 26, an unemployed laborer he met a few months ago. Borrego died at a hospital after being shot once in the abdomen.
Alan Brown, Rodriguez's attorney, called the shooting "very defensible" and said the singer thought Borrego was a burglar.
Police would not discuss a motive.
"Johnny was across the street at his brother's house," Brown told the San Antonio Express-News. "He heard noise, they had had problems with burglars."
Rodriguez entered his home through the front door and drew a gun from a shelf, Brown said. "It was dark," Brown said. "An intruder came toward him. He surprised Johnny."
Brown said Rodriguez realized whom the intruder was only after the single shot was fired.
"(Borrego) had been coming uninvited. He had been told not to be in the house," Brown said.
Rodriguez had his first Top Ten hit in 1972 with "Pass Me By (If You're Only Passing Through)." He moved to the top of Billboard's Country Hit List with "You Always Come Back (to Hurting Me)" and again when he wrote and recorded "Ridin' My Thumb to Mexico."
More than a dozen of the singer's albums and singles landed in the Top 10. But his career suffered when he began to abuse drugs and alcohol, Rodriguez has said.
Sabinal is a farming community 60 miles west of San Antonio.