Ono thanked Mojo for their "courageous" decision in giving her the first music prize of her career.
With Lennon, the Plastic Ono Band as as a solo artist, she has released over 20 albums in 41 years.
It's really great that I went on stage and people were very warm towards me, I didn't expect that.
Former Smiths guitarist Johnny Marr, who received a classic songwriter award, said Ono deserved the award after enduring "an awful lot of utterly terrible press that was completely uninformed and out of control for no reason".
Her records are pretty great. She didn't really need to be a Beatle wife. She was doing some pretty good stuff as it was, and I think she's fantastic.
Mojo editor Phil Alexander described Ono as "a huge influence on modern music".
She may have been married to one of the most famous men in the world, but she also helped change music as we know it in her own right.
First, by introducing avant-garde sensibilities to her husband but, just as significantly, by continuing to push the boundaries of what was deemed the norm way after that.
The Plastic Ono Band are due to perform at the Meltdown festival in London on Sunday.