Mike Gillis of the Vancouver Canucks, the league's top team during the regular season, and David Poile of the Nashville Predators, whose team has been in the playoffs six of the past seven seasons, were the other finalists.
The winner will be announced on June 22 at the NHL Awards in Las Vegas.
Yzerman, a Hall of Fame player who won four Stanley Cups with the Detroit Red Wings, including one as management, was hired by the Lightning last year and presided over a team that enjoyed a 23-point improvement over the 2009-10 season.
Gillis strengthened the Canucks defensively by adding blueliners Keith Ballard and Dan Hamhuis and shutdown center Manny Malhotra. The changes helped the team to a franchise-record 117-point season while allowing a league-low 185 goals.
Poile oversaw a Nashville team that boasts more than half of a lineup that was drafted and developed by the organization, including the team's top four scoring defensemen Shea Weber, Ryan Suter, Cody Franson and Kevin Klein.
Voting for the award was conducted by the league's 30 general managers and a panel of NHL executives, print and broadcast media.
(Reporting by Frank Pingue in Toronto)
Receive your weekly recap of all the happenings around the world of sports.