The recount slightly boosted Mr Moreno's margin over his conservative rival, Guillermo Lasso.
Mr Lasso had demanded a full recount citing allegations of fraud but the national electoral council only agreed to a recount of 10% of the votes.
Mr Moreno will be sworn in on 24 May.
The National Electoral Council said that following the recount Lenín Moreno had increased his lead over Mr Lasso by 0.01 percentage points.
Mr Moreno won with 51.16% against Mr Lasso's 48.84%, National Electoral Council President Juan Pablo Pozo said.
Mr Lasso dismissed the partial recount as a "show" and a "manoeuvre" by the governing party of Mr Moreno "to legitimise a process which has been less than transparent".
But monitors from the Organization of American States said they considered "a recount of this magnitude and under these norms to be an exercise in transparency".
Mr Lasso said he would give a news conference on Wednesday to announce how he will proceed next.
Mr Moreno will take over from President Rafael Correa, who has been in power since 2007.
He is expected to continue many of his predecessor's policies, including allowing Wikileaks founder Julian Assange to remain at the Ecuadorean embassy in London.
Mr Lasso had said that if he was elected he would kick out Mr Assange, who has been living at the Ecuadorean embassy since 2012 to avoid extradition to Sweden.
Following a recount of almost 1.3 million votes in Ecuador, the electoral council has confirmed left-wing candidate Lenín Moreno as the winner of the presidential poll held on 2 April.