European Council president Charles Michel. AFP
Simon Mordue, chief diplomatic advisor to European Council president Charles Michel, will chair the talks, Michel's spokeswoman said.
Azerbaijan and Armenia, along with EU heavyweights France and Germany, will be represented by their national security advisors.
The EU special representative for the South Caucasus, Estonian diplomat Toivo Klaar, will also attend.
Armenia and Azerbaijan have fought a 30-year conflict over the breakaway region of the Nagorno-Karabakh, mainly populated by ethnic Armenians.
But last week a lightning offensive by government forces established Azerbaijani control, and ethnic Armenian fighters have begun to disarm.
Tuesday's meeting in Brussels will be the first such encounter since the offensive, but the leaders of both countries are scheduled to meet next month.
Armenian Prime Minister Nikol Pashinyan and Azerbaijani President Ilham Aliyev will be at the European Political Community summit in the Spanish city of Granada on October 5.