Morales needed just over 50 percent to win outright and avoid the formality of congress deciding between him and the man who finished a distant second, Jorge Quiroga.
Bolivia's politicians and news media already considered the matter settled: Local newspapers refer to him as president-elect and the outgoing administration said it is preparing to hand over power.
The electoral court said turnout had averaged almost 85 percent, much higher than in previous Bolivian elections.
Morales would be the first president since Bolivia returned to democratic rule in 1982 to be directly elected at the ballot box, with no need for congress to choose.
He would also be Bolivia's first Indian president, marking a historic turning point in a country traditionally governed by the non-Indian elite.
Quiroga, a former president, was in second place with 30 percent. He has already conceded defeat.
President Eduardo Rodriguez's administration has said it is organizing a transition team in anticipation of Morales' inauguration on Jan. 22.
The 46-year-old Aymara Indian has vowed not only to halt U.S.-backed coca-eradication programs but to shake up Bolivia's political elite. Although Aymara and Quechua Indians make up a majority of the nation's population, people of mixed or European descent have until now governed the country.
Morales has said he would turn over "vacant, unproductive" land to poor farmers and expand Indian rights, while increasing state control of Bolivia's vast natural gas reserves.
On Tuesday, he said he would not allow free production of coca, but promised a study to determine if demand for legally grown coca warrants raising production.
Current laws permit coca cultivation in 29,000 acres of the Yungas valley and 7,900 acres in the Chapare region.
For thousands of years, people in the Andes have chewed coca to stave off hunger, made it into tea or used it as medicine.
Washington has offered congratulations but spoken cautiously about the victory of a man who described himself as the "nightmare" for the United States.
Future U.S.-Bolivia relations will be determined by the "behavior" of the new government in La Paz, Secretary of State Condoleezza Rice told CNN late Monday.
Morales has been a problem for Washington since he rose to prominence in the 1990s as the leader of the cocaleros, or coca farmers, in Bolivia's tropical Chapare region, leading their often violent resistance to U.S.-backed coca eradication efforts.
While the U.S. government insists that much of the Chapare's coca becomes cocaine, farmers say they supply a legal market. Coca leaves are sold in supermarkets and can be chewed, brewed for tea, and used in religious ceremonies.
Morales has said that he welcomes good relations with the United States but vowed ties with Washington would not be a "relationship of submission."
Two of his closest allies are Cuban President Fidel Castro and Venezuela President Hugo Chavez, whose ties with Washington have been increasingly strained.
On Monday night, Morales said in a telephone interview with Cuban television that he hoped to work with Castro for "social justice" in the region.