The June 1968 manifesto demanded openness from officials in the then Czechoslovakia and called for the resignation of those who misused power.
Two months later, Soviet-led forces invaded the country, ending hopes for political reforms.
Vaculik's novels include The Axe, The Guinea Pigs and The Czech Dreambook.
Vaculik - like his contemporary and fellow-writer Milan Kundera - initially supported the Communists when they took power in Czechoslovakia in 1948.
But in 1967, a year after he published his first major work, The Axe, he was expelled from the Communist Party, following a highly critical speech at a writers' congress.
However, a year later, he was asked to write his Two Thousand Words manifesto to support reformers within the Communist Party under the liberal leader Alexander Dubcek.
In 1970, he wrote The Guinea Pigs - a bleakly comic novel about the cynicism pervading everyday life in the years after the pro-Soviet crackdown.
Several years later, Vaculik was one of a group of dissidents who wrote the Charter 77 human rights manifesto, along with the playwright and future President Vaclav Havel.
After the 1989 Velvet Revolution, Vaculik was widely published and received a number of literary rewards.
"We will all remember him as an important and brave man of pen and word who was free and independent throughout his life and under any regime," said Czech Prime Minister Bohuslav Sobotka.
Czech novelist and former dissident Ludvik Vaculik, who wrote the Two Thousand Words manifesto during the 1968 Prague Spring, has died, aged 88.