He called on the country's governors and mayors "to work together to implement the new constitution".
The constitutional changes allow 36 indigenous groups to win the right to territory, language and their own "community" justice and limits the size of landholdings.
It also allows Morales to run for re-election and remain in power until 2014.
The changes were approved by 60 per cent of the votes cast, according to the Unitel television network. ATB television reported a 58-per cent approval.
The constitution has received little support in the opposition-controlled east of the country.
Exit polls showed that the referendum was defeated in the eastern departments of Santa Cruz, Tarija, Beni and Pando, hotbeds of activity against the president.
In Chuquisaca, Savina Cuellar, the provincial governor, held a rally and called on people to refuse to abide by the constitution, while Mario Cossio, Tarija's governor, called for negotiations with Morales.
Ruben Costas, the governor of Santa Cruz, told supporters at a rally that hundreds of thousands of Bolivians voted against the measure, and that this shows that the opposition had gained strength.
"The 'no' vote has put the brakes on the fools who wanted to destroy our country," Costas told his supporters.
Lucia Newman, Al Jazeera's Latin American editor, said: "Since the hundreds of laws that will make it possible to put this new constitution into practice still need to be written and passed by congress, Bolivia can expect more political turmoil ahead."
Elections: Presidents allowed two consecutive five-year terms
Indigenous rights: Recognition of self-determination of 36 'nations' and sets aside seats in Congress
Natural resources: State control for all gas, oil and mineral reserves
Local autonomy: Gives authority to state assemblies that control local issues and self-rule for indigenous groups on traditional lands
Justice: High court judges to be elected rather than appointed
Equality: Prohibits discrimination on sexual orientation and guarantees freedom of religion
The eastern Bolivian governors are seeking increased autonomy and more authority over the mineral resources - especially oil and gas - found in their regions.
Some Catholic and evangelical clerics have also opposed the referendum, fearing that the new constitution's declaration that the country is "independent" from religion could pave the way for abortion rights and gay marriage.
Ahead of the vote, Alvaro Garcia Linera, the vice-president, made it clear that the national result was binding and applied to all Bolivians.
Although Morales is widely popular, his rise and the constitutional change have heightened divisions in the country, which erupted in violence in September when 20 indigenous government supporters were killed.
The opposition, led by state governors in the country's more prosperous east, are concerned by Morales's leftist ideals and fear he is taking Bolivia into the orbit of Hugo Chavez, Venezuela's president and a vocal critic of the US.
Morales's nationalisation of the telecommunications and gas sectors has scared off foreign investors, worsening state finances that are now also battered by the global economic crisis.