"You guys deserved to be here but I was more lucky," Jagr said to the other finalists at ceremonies at the Hockey Hall of Fame.
"I said it last year and I'm going to say it again: This trophy is very special to me because it's voted by the players."
The voting was the closest in the award's 30-year history. Jagr received 192 votes to 159 for Bure and 129 for Pronger.
All three also were finalists Thursday night for the Hart Memorial Trophy, the player judged most valuable to his team as chosen by the Professional Hockey Writers' Association.
Jagr is the second Penguins player to win the award more than once. Mario Lemieux, now the team's owner, won it four times.
For winning, Jagr receives $20,000 to donate to a grassroots hockey program of his choice. The other finalists each receive $10,000 to donate.
Jagr won his third straight scoring title with 42 goals and 54 assists despite missing 19 games because of injuries. He averaged a league-best 1.52 points per game.
Bure led the league in goals with 58 and finished two points behind Jagr in the scoring race.
Pronger led the NHL in minutes played with an average of 30 minutes, 14 seconds per game. He had a plus-minus of plus-52 and had career highs in goals with 14 and assists with 48.
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