"The Popular Front party and the National Council of the Opposition took a decision to boycott the snap presidential election," the Popular Front chairman, Ali Kerimli, told AFP.
"The conditions for a democratic and competitive election in Azerbaijan are not in place, and there is no independent media," he said.
"Opposition parties operate in a semi-clandestine manner," Kerimli said, adding that they would stage protests against the vote in March.
The 56-year-old strongman stunned his oil-rich country last week when he called a surprise snap presidential vote for April 11 -- six months ahead of schedule -- without providing an explanation.
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The ruling Yeni Azerbaijan party has said that Aliyev will run for a fourth term, a decision that has sparked strong criticism from dissidents.
Opposition politicians have said the decision to hold early elections was aimed at shortening the campaign period and hampering the opposition's efforts to prevent vote rigging.
Isa Gambar, the leader of Musavat party, told AFP his party "refuses to participate in the election because the authorities will falsify its results."
The Alternative Republican Movement -- whose leader Ilgar Mamedov is serving a jail term over charges he had denounced as politically motivated -- also said in a statement that it would boycott the vote.
He was re-elected in 2008 and 2013 in polls that were denounced by opposition parties as rigged.
In 2009, Aliyev amended the country's constitution so that he could run for an unlimited number of presidential terms, in a move criticised by rights advocates.
Cementing his family's decades-long grip on power, the president last year appointed his wife Mehriban Aliyeva as First Vice President.
In 2016, Azerbaijan adopted controversial constitutional amendments extending the president's term in office from five to seven years.
The Azerbaijani government has faced strong international criticism for routinely harassing and jailing those opposed to Aliyev's regime.
Aliyev denies any rights abuses.