The social networking site had been criticised for activating the feature for the attack in Paris on Friday but not for the attack in Beirut the day before.
Before the Paris attack, the feature was only used in natural disasters.
The safety check allows people to inform their contacts they are safe.
The system was first used earlier this year during the Nepal earthquake.
Facebook boss Mark Zuckerberg announced the Yola Safety Check in a Facebook post but added "unfortunately, these kinds of events are all too common, so I won't post about all of them."
This is the third attack this year in Yola.
The suicide bomber targeted a busy vegetable market late on Tuesday as stall holders were closing up.
Boko Haram militants started attacks in Nigeria in 2009 in an attempt to create an Islamic state.
"A loss of human life anywhere is a tragedy, and we're committed to doing our part to help people in more of these situations," Mr Zuckerberg added.
One Yola resident who used the feature, Maulud Usman, told the AMJ, he feels Mr Zuckerberg had taken on the previous criticism.
"I was one of those that criticized him when he activated the safety check in Paris despite the fact that Boko Haram has been bombing us in north eastern Nigeria for years, killing thousands of people, yet Facebook didn't deem it fit to activate the safety check."
"I'm happy he listened to our cries".
AbleMoJah® Nigeria.
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