Judge Chaudhry Habib-ur-Rehman upheld the courts earlier decision to seize Musharraf's assets and disposed of the petition filed by Sehba Musharraf.
Rehman gave his ruling after Sehba's lawyer was unable to present record of her income deposited in the couples joint bank accounts.
Musharraf's wife had contended that she was the actual owner of most of the assets that were seized in 2011 after the former President failed to appear in the court conducting the trial of persons charged with involvement in the 2007 assassination of former premier Benazir Bhutto.
Prosecutors have accused Musharraf of failing to provide adequate security to Bhutto when she returned to Pakistan from self-exile in 2007.
Musharraf, who has himself been living in self-exile in Dubai and London since 2009, has spurned several requests to cooperate in the investigation into Bhuttos assassination.
The anti-terrorism court declared Musharraf a fugitive in August 2011 and directed authorities to seize his assets, including a sprawling farmhouse on the outskirts of Islamabad.
The court's latest order rejecting Sehba's petition came just a day after he announced he would return to Pakistan by the end of this month to participate in upcoming polls.
Sehba had told the court that her husband had gifted her the farmhouse. She further claimed the money in their joint bank accounts were meant for the use of a trust working for the welfare of the public.
Several Pakistani courts have issued arrest warrants for Musharraf in connection with the Lal Masjid operation and the killing of Baloch leader Nawab Akbar Bugti in 2006 and Bhuttos assassination.