He said: "Of course there are similarities between the OPT [Occupied Palestinian Territory] and apartheid South Africa."
He also told the council that the situation "places in danger the whole international human rights enterprise".
He said that Western states would never rally support among developing nations for effective action against perceived abuses elsewhere, such as Sudan's Darfur, unless they tackled the plight of Palestinians.
Israel dismissed the statement and Dugard's regular reports to the council as "one-sided, highly selective and unreservedly biased".
Dugard, who was appointed to his position in 2001, said that Gaza was an imprisoned society and that the situation in the West Bank was little better.
'Reign of terror'
He said about 500,000 Israeli settlers were now living in the West Bank and East Jerusalem, territories seized by Israel during the 1967 Middle East war.
"Settlers, largely unrestrained by the Israel Defence Forces [the Israeli military], subject many Palestinians to a reign of terror - particularly in Hebron," he said.
Itzhak Levanon, Israel's ambassador to the UN in Geneva, said such language was "inflammatory and inciteful" and would not contribute to a "process of constructive dialogue between Israel and the Palestinians".