"However, we do note the concerns about the electoral process and expect that they will be fully considered and resolved in a legal and transparent manner," the US State Department said.
Moreno's victory in the April 2 runoff has been disputed by conservative candidate Guillermo Lasso, who has charged fraud and demanded a recount.
"The United States congratulates the people of Ecuador on taking part in the second-round Presidential elections on April 2. We also congratulate Lenin Moreno of the Alianza Pais party on his victory," the State Department said.
"We look forward to working with the new government to build a constructive relationship in areas of mutual interest."
The United States has had a contentious relationship with outgoing President Rafael Correa, a fiery critic of Washington who aligned Ecuador with a leftist bloc in Latin America led by Venezuela.
Correa, who is stepping down after 10 years in office, threw his support behind Moreno, an affable wheelchair-bound politician who has championed disability rights as Correa's vice president.