Haftar also expressed his gratitude for the position Tunisian President Beji Caid Essebsi has taken regarding the crisis in Libya, his tireless efforts to reach a local solution, as well as the Tunisian peoples' support of the Libyan people.
The military commander backs a rival administration based in eastern Libya that is refusing to recognize the authority of the Tripoli government.
Meanwhile, protestors took to the streets in Mistrata on Friday, many wearing yellow vests, to denounce Haftar's assault on the capital as well as the involvement of foreign powers in Libya's internal affairs.
The White House did not say why it delayed giving news of the phone call.
Trump's about-turn flied in the face of his Secretary of State Mike Pompeo who earlier this week called on Khalifa Haftar to stop his advance on Tripoli.
Al Jazeera's Mahmoud Abdel Wahed, reporting from Tripoli, said while GNA forces claim Haftar's fighters were on the retreat, the battle would not be easy "because Haftar's forces are supported by regional powers, like Egypt, Saudi Arabia and the United Arab Emirates".
Until recently, the Trump administration had distanced itself from the United Nations push for the national reconciliation between the internationally-recognized administration of Prime Minister Fayez al-Sarraj and Haftar, exercising a more limited role that primarily focuses on fighting the Islamic State (ISIS/ISIL), al-Qaeda, and other jihadis.
In recent months, however, the Trump administration seems to be warming to General Haftar and his LNA although the US has officially backed the GNA throughout the conflict, the New York Times (NYT) alleged citing anonymous foreign diplomats early this month.
Mr Trump's call suggests he endorses Gen Haftar, unlike some of his allies.
The offensive, which Haftar said was aimed at cleansing Libya's western region of "remaining terrorist groups", has raised fears of a full-blown civil war in the oil-rich country, which has been mired in chaos since the NATO-backed toppling of long-time ruler Muammar Gaddafi in 2011.
France dismissed the allegation even after it recently moved to prevent the European Union (EU) from condemning Haftar's push into Tripoli. "We, the Libyan people, are against Trump and against Haftar".
On Thursday the UN-backed Prime Minister Fayez al-Serraj condemned the "silence" of his global allies amid the assault by Gen Haftar's forces.
Who supports the Tripoli government?
Foreign powers are anxious but unable to present a united front over the latest flare-up in the cycle of anarchy and warfare that has gripped Libya since dictator Muammer Qadhafi was toppled in 2011.
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