The Muslim teenager disappeared from home in Warrington, Cheshire, in 2003 and it was feared she was being forced into marriage.
Her decomposed remains were discovered in Cumbria five months later after heavy flooding swept away the undergrowth her body had been hidden in on by the River Kent at Sedgwick.
Her father, Iftikhar, 50, and mother, Faranza, 47, have always denied any involvement.
The couple were arrested on suspicion of murder at their home on Thursday but have now been released from custody, Cheshire Police said.
An inquest into her death heard Shafilea was last seen alive, doing her homework at home, on September 11, 2003. The 17-year-old was reported missing a week later by a former school teacher.