He lost the referendum but the government rejected the result and Morales is set to stand in October's election after the constitutional court, filled with government loyalists, ruled in his favor.
Bolivia's 2009 constitution, which Morales himself promulgated, limits a president to two consecutive terms of office.
But the constitutional court said it was Morales's human right to seek reelection.
He won his party's primary last month, after which he declared the 2016 referendum result "buried."
"The only thing that is buried here is an illegal candidacy, for which the public won't vote," said Carlos Mesa, a former president and opposition leader whom polls place as the nearest challenger to Morales.
Already the longest-serving president in Bolivia's history, Morales has been in power since 2006.