Nauert's nomination had been rumoured for weeks, and she had started handing over some of her responsibilities as spokeswoman to her deputy, Robert Palladino.
She became the spokeswoman to the State Department in 2017.
Mr Trump will make the announcement in the coming hours that State Department spokeswoman Heather Nauert will take up the plum role, Bloomberg reported, citing three sources.
The 46-year-old former SC governor - one of the few women in the Trump cabinet - gave no reason for leaving, but dismissed speculation she was planning to run for president in 2020.
Sources told Fox News Thursday evening that he will announce his decision in a tweet Friday.
Plucked from Fox by the White House to serve as State Department spokeswoman, Nauert catapulted into the upper echelons of the agency's hierarchy when Tillerson was sacked in March and replaced with Mike Pompeo.
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For his work on "SNL", Samberg earned an Emmy Award and six additional nominations. He hosted the Emmys in 2015 and the Film Independent Spirit Awards in 2013.
"She's excellent. She's been with us a long time", Trump said of Nauert last month.
Trump had previously said Nauert was under serious consideration to replace Haley, though he's been known to change course on staffing in the past.
Nuart was brought on to the administration after providing commentary on "Fox and Friends" on what appears to be Trump's favorite cable news network.
She would be taking the position amid a roster of thorny global challenges, ranging from North Korea's nuclear program to Yemen's starvation and the growing divide between the United States and its closest allies over the Iran nuclear deal, climate change and other issues. But she has said she would not be running for the top job in 2020, when Trump plans to run for a second term.
The president considered Nauert for the position among a list of potential nominees that included former White House aide Dina Powell and ambassador to Germany Richard Grenell.
Haley has been the USA ambassador to the United Nations for the entirety of Trump's presidency.