The 38-year-old had officiated top-flight matches in his native Russia since 2003, and was one of his country's most decorated referees.
After the weekend clash between Dinamo Moscow and Rubin Kazan, the plane he caught en route to Petrozavodsk crashed upon landing in heavy fog early on Tuesday.
"Pettai established a reputation as of the best and most experienced referees in our country," read a statement on the Russian Football Union's official website.
"Our sincere condolences to the friends and relatives of all the victims. We are with you throughout these hard and painful minutes."
Pettai is survived by his wife and two children, and the football federation said it would provide assistance to his family.
"We will help the family, without a doubt," RFU chief Sergei Fursenko said, according to Russian news agencies.
"He was a person who dedicated himself to football. He has a wonderful family."
Pettai began his professional refereeing career in 1996, after playing for his local side as a midfielder.