Counting is underway and the results of the poll are expected to be announced later on Friday, with a voter turnout of almost 80 percent.
A “yes” vote would endorse government plans to grant an amnesty to many of those jailed over the killings.
Algerian media has pointed out that voter turnout is the real test of the peace charter referendum and predicted a “yes” result.
However opposition and human rights groups have called for voters to reject the charter, saying it sweeps years of suffering under the carpet and is simply a pretext to give the president new powers.
They want authorities to account for around 7,000 people who disappeared during the conflict.
The conflict erupted in 1992 when the Algerian military cancelled the 1992 election which Islamic fundamentalists were poised to win.
President Bouteflika launched a “civil reconciliation” initiative at the start of his first term in 1999, leading to a partial amnesty for thousands of Islamist rebels.
However the government estimates about 1,000 armed extremists remain active.
The leader’s Charter for Peace and National Reconciliation aims to modernise Algeria and strengthen its ties with the West.
It offers compensation to the families of victims, but ends legal proceedings against those jailed for perpetrating the violence.
Only “those involved in mass massacres, rapes and bomb attacks in public places” would be excluded from the amnesty.
Analysts predict the vote will approve the charter because Algerians are tired of war and want to look to the future.
Amnesty International, the London-based rights group, said the charter absolves the military of their part in human rights abuses and would prevent other crimes from being probed.
Algeria’s opposition Socialist Forces Front (FFS) said it “cannot endorse a text that glorifies force and deprecates political mediation, consecrates impunity and amnesty, and in the end negotiates away pain and suffering”.