The Pentagon described the call between General Raymond Odierno, chief of staff of the US Army, and Gen Prayuth as constructive and added he believed the conversation took place late on Thursday.
"The general made it clear that we certainly expect a return to democratic principles in Thailand just as soon as possible," Pentagon spokesman Rear Adm John Kirby said.
Asked why the call was made by Gen Odierno, who was the first US military official to have direct contact with Gen Prayuth since the coup, Rear Adm Kirby said: "The Thai army chief, the one who announced that they were suspending the constitution, is in effect Gen Odierno's counterpart."
"So it just made sense that he would be the one to have that conversation."
The United States swiftly condemned the coup on Thursday and has said it is reviewing its aid to Thailand. On Friday, the US State Department said it had already suspended about $3.5 million in military aid, including a portion for training.
The State Department also recommended on Friday that US citizens reconsider any non-essential travel to Thailand, particularly Bangkok, due to the ongoing unrest.
The United States has about 700 marines and sailors in Thailand for military drills that had been slated to run through May 27. Rear Adm Kirby said the US forces were still in Thailand.
He acknowledged that the drills had not yet been cancelled but it was unclear to what extent actual training may have been affected by the unrest.
Speaking broadly about ties with Thailand, Rear Adm Kirby noted that "this is a military that we have a longstanding relationship with, going well back in United States history."
"And it's a military-to-military relationship that we still believe is important," Rear Adm Kirby said.
"But circumstances are different in Thailand, and this was a conversation that needed to happen."