The 34-year-old was named the Latin Recording Academy Person of the Year at the special tribute Wednesday.
Shakira wiped away tears as Mebarak sang the classic song Mi Nina Bonita (My Pretty Girl), while pictures of the father and daughter appeared on a big screen behind him, reports femalefirst.co.uk.
"Thank you, daddy, for that song," the 34-year-old later told him.
Also present at the occasion were Black Eyed Peas rapper Taboo and Mexican rocker Alejandra.