Both countries' leaders have recently said that they were closer than ever to the signature of a comprehensive peace deal, following years of fruitless internationally mediated negotiations.
"Armenia and Azerbaijan have an opportunity to achieve an enduring peace," Stoltenberg said during a press conference in Yerevan alongside Armenian Prime Minister Nikol Pashinyan.
"I urge both countries to reach an agreement paving the way for normalisation of relations and a durable peace for your people," he added.
Stability in the volatile Caucasus region "matters for the Euro-Atlantic security."
Last year, Azerbaijan carried-out a lightning military operation in Karabakh that saw Baku recapture the mountainous enclave from Armenian separatist forces who had controlled it for three decades.
In the aftermath, the entire Armenian population fled Karabakh for Armenia.
Yerevan was the last leg of Stoltenberg's three-day Caucasus tour during which he also visited Azerbaijan and Georgia.
During his visit to Georgia on Monday, Stoltenberg called on the NATO-hopeful Black Sea nation's government to consolidate democratic reforms ahead of parliamentary elections scheduled in October.
On Sunday in Baku -- which is set to host the COP29 UN Climate Change Conference in November -- he stressed the need to fight global warming, saying climate change undermines global security.
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