The Saudi minister said winning the war against terrorism would require more than military confrontation with militants.
"Confronting terrorism requires an intellectual offensive so as to mitigate fanaticism and fundamentalism," added Prince Nayef, after the two sides inked the agreements. "Thought is only faced by thought."
Saudi Arabia has been rocked by a series of bloody attacks over the past two years, which mostly targeted the kingdom's expatriate community, leaving many dead and injured.
Many of the strikes were claimed by groups linked to the Al-Qaeda network of Saudi dissident Osama bin Laden, whom the United States accused of masterminding the September 2001 attacks on its soil.
Bin Laden and his henchmen spent some time in Sudan in the mid-1990s when the country's Islamist rulers played host to Muslim fundamentalists from around the region and beyond.
Khartoum remains on Washington's list of terrorist-sponsoring countries and until the late 1990s was considered the black sheep of the region for its alleged support for Islamist terrorists.
Prince Nayef described his three-day visit to Sudan as being "successful", saying it had "achieved its goals."