Brayden Point (fourth playoff goal), J.T. Miller and Anton Stralman each had goals and Andrei Vasilevskiy made 27 saves for the Lightning, who will face either the Washington Capitals or Pittsburgh Penguins.
Boston won the series opener 6-2 in Tampa but was outscored 15-7 in the next four games.
"No one probably would have predicted, including ourselves, that we'd beat a team of that quality in four straight games, but we found a way and it feels good," Lightning captain Steven Stamkos told NBC after the game.
David Krejci scored for Boston. Tuukka Rask recorded 19 saves.
The Bruins fell to 0-23 all-time when trailing 3-1 in a best-of-seven series.
"We scored against Toronto, so it's not like after 89 games we forgot how to score or not playing the right way," Bruins coach Bruce Cassidy said after his team was outscored 17-13 in the series. The Bruins scored 28 goals in their seven-game, first-round series against the Maple Leafs.
The Lightning won the Atlantic Division and finished with the top seed in the Eastern Conference. Tampa Bay also defeated the New Jersey Devils in a five-game, first-round series before dispatching Boston.
Tampa Bay lost to the Penguins in a seven-game series in its last trip to the conference finals in 2015-16. One year prior, the Lightning bested the New York Rangers in seven games before losing to the Chicago Blackhawks in the Stanley Cup Finals.
Krejci opened the scoring with 48 seconds left in the opening period. Boston had been 22-2 in playoff games when Krejci scored a goal.
Tampa Bay scored twice in the second, with Point connecting at 10:43 and Miller adding his goal at 14:00.
The Bruins had one last chance after David Pastrnak was tripped by Ryan McDonagh with 4:18 remaining in the third, but the Lightning killed off the penalty.
Stralman added an empty-netter with 1:29 left.
Boston's David Backes was ruled out of the game early in the third after taking a head-to-head hit from Miller in the second period.
--Field Level Media
Boston | Tampa Bay | |
David Krejci 1 | Points | J.T. Miller 1 |
David Krejci 1 | Goals | J.T. Miller 1 |
Patrice Bergeron 1 | Assists | Victor Hedman 1 |
David Krejci 1 | Power Play Goals | J.T. Miller 1 |
N/A | Short Handed Goals | N/A |
Tuukka Rask .905 | Save Percentage | Andrei Vasilevskiy .964 |
Tuukka Rask 19 | Saves | Andrei Vasilevskiy 27 |