The two also discussed latest developments in the region, Mehr News Agency (MNA) reported.
Heading a high-ranking delegation, Araqchi is on a tour to Azerbaijan, Armenia and Russia to present Iran’s initiative for a peaceful settlement of the conflict between Armenia and Azerbaijan over the Nagorno-Karabakh region.
Araqchi, as the especial envoy of Iranian President Hassan Rouhani, said Iran has always opposed the occupation of the territories of the Azerbaijan Republic and supported the territorial integrity of that country.
Aliyev, for his part, pointed to the month-long military conflict between Azerbaijan and Armenia, noting that the former will liberate its lands from occupiers and establish the standards of international law and justice there.
Referring to the two-day missile attack by Armenian forces on the city of Barda in the Azerbaijan Republic, Aliyev said that 21 civilians were killed and more than 70 wounded in the attack that was carried out on Wednesday.
He said that Armenia has violated the ceasefire agreement brokered by Russia earlier this month.
After the meeting, Araqchi described his consultation with the Aliyev as positive and constructive.
He told reporters, "Today, in a long positive and constructive meeting, I presented the regional plan of Iran to help end the conflict in Nagorno-Karabakh to the President of the Republic of Azerbaijan."
Speaking before leaving Baku for Moscow, Araqchi said that Baku welcomed Tehran's initiative.
Earlier in the day, Araqchi held separate meetings with Azerbaijani Foreign Minister Jeyhun Bayramov and Deputy Prime Minister Shahin Mustafayev.
Armenia and Azerbaijan have been locked for decades in a conflict over Nagorno-Karabakh, an ethnically Armenian area of Azerbaijan which broke away from Baku in a 1990s war.