The militants killed Lt Col Muhammad Abu-Ali on Friday.
The 36-year-old was one of five soldiers killed by Boko Haram fighters who attacked a military base in Mallam Fatori, northern Borno State.
Boko Haram has been fighting the Nigerian army in its quest for an Islamic state in northern Nigeria.
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Col Abu-Ali was nicknamed Sarkin Kaki, which is Hausa for war king, and was promoted rapidly through the ranks to Lieutenant Colonel after he was one of those who led the operation to re-take the town of Baga from Boko Haram.
Hundreds of people were massacred by Boko Haram in Baga in January 2015 when the army ran away from the town in what was regarded as the worst attack of Boko Haram's insurgency.
But in February of that year the army retook the town.
In early 2015, Boko Haram controlled much of Borno State but it has now been pushed out of most of these areas.
A journalist who reported from the area at the height of the insurgency wrote that he couldn't stop crying at the news of Col Abu-Ali's death.
Hamza Idris called him a fallen hero whose life was full of gallantry:
"He came, he saw, he conquered and cleared the ruins for the next generation."
Nigerian President Muhammadu Buhari tweeted his tribute to the commander.
"No words can do justice to the patriotism and remarkable courage of these soldiers, who laid down their lives for Nigeria."
"I call on members of the Armed Forces to not allow this tragic incident dampen their spirits and resolve. Evil will not triumph over good," he added.
Tributes are being paid to a Nigerian army commander nicknamed "war king" after he was killed by Islamist militants Boko Haram.