Lucas Zelarayan and Derrick Etienne scored during a dominant first half by the hosts at MAPFRE Stadium, where the former sealed the win in the 82nd minute.
Seattle – playing their fourth MLS Cup in five years – improved in the second half, but Crew were too good.
Columbus, in their first decider since 2015, became the seventh team in history to win the MLS Cup more than once.
Crew made the stronger start and Gyasi Zardes forced an excellent reaction save from Stefan Frei in the 17th minute.
Just eight minutes later and Crew went ahead, Zelarayan squeezing a volley under Frei after Harrison Afful's cross from the right.
Columbus doubled their lead just after the half-hour mark, Zelarayan picking up a poor clearance before laying off to Etienne, who placed a smart side-footed finish into the bottom corner.
Crew became the first team since DC United in 2004 to hold a multi-goal lead at half-time of the MLS Cup, according to Opta.
The Sounders pushed in the second half and Jordan Morris hit the crossbar in the 80th minute for the defending champions.
But Columbus sealed their win through the impressive Zelarayan, who powered a finish into the top corner after a fine run by Luis Diaz Espinoza.
Zelarayan became the second player to be involved in three goals in a single MLS Cup, joining Guillermo Barros Schelotto, who achieved it with Columbus in 2008.