Bush angered the Saudi government last month by rejecting its request to declassify part of a congressional report on the September 11, 2001, attacks dealing with Saudi Arabia.
White House spokesman Scott McClellan said Bush discussed progress in the “war on terrorism” as well as bilateral relations during his 20 minute call from his Texas ranch with the crown prince on Saturday.
"It was a good, positive conversation," McClellan told reporters. "They talked about the overall close cooperation in our efforts to crack down on terrorism and the two leaders talked about how strong relations are between the United States and Saudi Arabia."
The congressional report on the September 11 attacks was released with a portion on Saudi Arabia still classified. The report raised suspicions over possible links between individuals in the Saudi government and some of the hijackers, 15 of whom were Saudis.
During a visit to the White House last month, Saudi Arabia's foreign minister angrily denounced the report as an "outrage" that "wrongly and morbidly" accused his country of complicity in the attacks.
Bush refused to declassify the section dealing with Saudi Arabia on the grounds it would compromise intelligence.
In another show of solidarity between the two nations, US Central Command chief General John Abizaid met in Jeddah on Saturday with Saudi Defence Minister Prince Sultan bin Abd al-Aziz and his assistant Prince Khaled bin Sultan, the official SPA news agency reported.
Saudi Arabia has turned down a request by the United States to dispatch peacekeeping troops to Iraq.
Abizaid, on his first visit to Saudi Arabia since his appointment as head of Central Command on 7 July, discussed "issues of mutual interest" during separate meetings with the Saudi officials, the agency reported.
The kingdom's chief of staff General Saleh al-Muhaya and commanders of the armed forces attended the two meetings. The US ambassador to Saudi Arabia Robert Jordan was also present.
Riyadh and Washington agreed in May to withdraw several thousand US troops which had been stationed in the kingdom since the end of the 1991 Gulf War, following a visit by US Defence Secretary Donald Rumsfeld.
Washington subsequently moved a state-of-the-art command and control centre from Prince Sultan Air Base in al-Kharj, south of Riyadh, to neighbouring Qatar.
Saudi Arabia has turned down a request by the United States to dispatch peacekeeping troops to help US forces in Iraq.
Abizaid, a Lebanese-American and Middle East expert fluent in Arabic, replaced General Tommy Franks as head of Centcom, which directs forces across a vast region that includes Iraq and Afghanistan.
Soon after his appointment, Abizaid said that in the face of constant attacks employing "guerrilla tactics", US troops in Iraq could expect a longer stay than anticipated.