Professor Oded Goldreich received the Israel Prize in Mathematics and Computer Science after a year-long battle with Education Minister Yifat Shasha-Biton.
The minister declined to be on hand for the ceremony.
Last month, the Supreme Court overturned a unanimous decision by the prize's committee stripping Goldreich of the prize.
“A person who calls for a boycott of an Israeli academic institution is not worthy of a state prize, no matter what his achievements or political views are,” Shasha-Biton told the court following the ruling.