NATO's Resolute Support advice and training mission was supposed to end this year but Taliban battlefield successes, especially their recent brief capture of the northern city of Kunduz, prompted a radical re-think.
"Today, NATO allies and Resolute Support operational partners have agreed to sustain the Resolute Support presence ... During 2016," Stoltenberg said after alliance foreign ministers endorsed the decision.
"The mission ... Will continue to be kept under review and, if necessary, will be adjusted to ensure its effectiveness."
US-led NATO invaded Afghanistan in 2001 shortly after the 9/11 terror attacks to oust the Taliban from Kabul. US troop numbers peaked at around 90,000.
The alliance ended combat operations at the end of 2014, leaving in place the Resolute Support mission.
Taliban militants are still mounting attacks while the Islamic State is gaining a foothold in the country.
Stoltenberg said NATO had compelling reasons to complete its mission in Afghanistan with a stable government in place able to ensure security.
"We are in Afghanistan to prevent Afghanistan becoming again a safe haven for terrorists. If Afghanistan becomes a safe haven, that will also be a threat to us," he said.
US President Barack Obama announced in October after the Kunduz attack that he would keep the bulk of the some 10,000 US troops in Afghanistan for another year because Afghan forces "are still not as strong as they need to be.
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