In December, Ghani announced Atta Mohammad Noor, one of the last remaining Afghan regional strongmen, had resigned as governor of Balkh province and a successor had been appointed, although it appeared to be more of dismissal after months of public wrangling between the two.
Atta, however, has refused to step down.
It was noted with surprise in Afghan government circles Pence referred to Atta as the governor. The call was seen here as an attempt to forestall military action by Kabul to permanently remove him and install his appointed replacement.
Bashir Bezhen, an Afghan security analyst, said after Pence's call, there was little chance of military action, which would have pitted the army against Atta's thousands of heavily armed supporters.
"There was fear before the phone call that the government will resort to a military move to oust Atta, and his supporters would respond with force," he said. "Now that fear is gone." He added referring to Atta as governor was a blow to the government from a legitimacy point of view.
Atta served as governor for more than 13 years in Balkh, a key province that serves as the gateway to Central Asia. He grew immensely rich in his position and is said to have run the province as his personal kingdom. He was also a key ally to the United States in the fight against the Taliban.
Atta's party, the influential Jamiat-i-Islami, welcomed Pence's comments — the first by a U.S. official on the issue. The Afghan government has not publicly responded to Pence's statement.
The president's conflict with the powerful regional strongman comes against a backdrop of upcoming elections, increased attacks by the Taliban and the Islamic State, and rising ethnic tensions in the country's diverse politics.
Members of Atta's Jamiat party are predominantly from the Tajik ethnicity, while Ghani is an ethnic Pashtun.
U.S. forces have also vastly increased their airstrikes against the Taliban under new rules of engagement that seek to force the insurgent group to the negotiating table.