The Edinburgh club made their move on Friday, following the end of the Clydesdale Bank Scottish Premier League season.
A statement on the Motherwell website read: "Motherwell Football Club can today confirm that it has received an official from Heart of Midlothian Football Club, seeking permission to speak with current manager Mark McGhee about the vacant managerial role at Tynecastle.
"After consideration, the Motherwell FC Board of Directors have decided to refuse this request."
The approach from Hearts came as no great surprise, with their interest in McGhee having been well known.
McGhee had claimed on Thursday night he would need to think "long and hard" about turning his back on Motherwell as speculation over his future mounted.
After his side's impressive 2-0 win at Hibernian, he insisted he had no plans to leave Fir Park and had not spoken with Hearts.