Azerbaijani state media said earlier on Wednesday that Aliyev had decided against attending the EU-brokered event in Spain where he could have held talks with Pashinyan.
Azerbaijani news agency APA reported that Aliyev would not attend the meeting, scheduled for Thursday, because of the "anti-Azerbaijani sentiment" of other summit participants.
Azerbaijan's authoritarian government captured Nagorno-Karabakh at the end of September after two days of fierce fighting.
About 100,000 inhabitants, almost all of them ethnic Armenians, have since fled the region for Armenia.
The disputed territory is within Azerbaijan's internationally recognised borders but was, at least until recent days, populated largely by ethnic Armenians.
Russia's Interfax news agency Interfax cited Pashinyan as saying he regretted missing the opportunity to hold talks with Aliyev and saying he had been ready to sign what he called a "breakthrough" document related to the two countries' peace talks.
The five-way meeting with the leaders of France, Germany, Armenia, Azerbaijan and EU Council President Charles Michel was meant to take place in Granada, Spain, on Thursday.
with DPA
