The mission is expected to continue over the coming days with plans in place for the arrival of additional teams from other hospitals next week.
Israel's defense connection with Azerbaijan is believed to have contributed to Baku's capabilities.
The medical delegation was sent on behalf of the Health Ministry to provide medical treatment to the hundreds of injured citizens.
The World Jewish Center in Armenia was vandalized. The attackers left a note saying "the Jews are the enemies of the Armenian nation."
Almost all the 120,000 or so inhabitants of Karabakh have since fled to Armenia, fearing for their safety.
Armenian officials say they have reason to believe that Azerbaijan may strike inside Armenia, despite denials.
Pope Francis called for talks between Armenia and Azerbaijan
"The situation often involves families arriving with children so weak that they have fainted in their parents' arms," an aid representative said.
In an exclusive interview, ambassador Arman Akopian describes the situation in Nagorno-Karabakh from his country's perspective.
Azerbaijan says it will respect the rights of ethnic Armenians who choose to stay, but that it has destroyed the concept of a breakaway state forever.