Kovalchuk and defenseman Anssi Salmela were dealt in exchange for defenseman Johnny Oduya, right wing Nicklas Bergfors and forward Patrice Cormier. Atlanta will also receive a first-round draft pick.
Earlier in the day, Atlanta General Manager Don Waddell announced Kovalchuk had rejected a series of proposals from the Thrashers. One would have paid Kovalchuk $101 million over 12 years.
Kovalchuk is in the last year of his contract and would have become an unrestricted free agent on July 1.
Atlanta has made the playoffs just once in Kovalchuk's eight-year career. New Jersey has won the Atlantic Division three of the last four years and leads the division again this season by one point over Pittsburgh.
Kovalchuk has scored 50 goals twice and he has 31 goals with 27 assists in 49 games this season. He is Atlanta's all-time leader in almost every offensive category, including goals (328), assists (287) and games played (594).