Rudi Effendi and his wife Nuriah also ate the victim’s genitals after the man was killed, police said.
The couple were being held for further investigation after their arrests at their house in Tulang Bawang district in Sumatra’s Lampung province on Sunday, a Lampung police spokeswoman said.
Police found the victim’s body in a burnt minivan on October 4, the spokeswoman said, adding that a month-long investigation led to the conclusion that the couple had planned to kill the man, who was a driver for a travel agency.
The couple had married in September and the husband found out on the wedding night that his wife was no longer a virgin.
She then said she had been raped one week before the marriage.
Police said Mr Effendi, 30, asked his 20-year-old wife to arrange a meeting with the man she accused of raping her.
He stabbed the man to death and cut off his genitals before setting the car on fire.
He said that he fried the severed genitals and ate them to cure his heartache over the rape.
Police said the couple could be charged with premeditated murder, which carries a maximum death penalty.