Spanish newspaper Sport reports that Susana Modric was kidnapped on Monday, although the motive behind it and the subsequent murder remain unknown.
Her body was found two days later in the boot of a car, and police have now opened an investigation into the incident.
The 40-year-old, who leaves behind two children, had been living in El Salvador for six years.
The news comes just two days after Luka Modric had helped Real Madrid overturn a two-goal deficit against Wolfsburg to reach the semi-finals of the Champions League.
The Croatia international was absent from training today and is now expected to miss his side's La Liga match against Getafe on Saturday.