Heatley became the first player with consecutive seasons of at least 50 goals since Pavel Bure did it with Florida in 2001 and 2002. Heatley also had exactly 50 last season, his first with Ottawa.
The Senators will open their best-of-seven Eastern Conference quarter-final series at home against Pittsburgh. They needed just a win to clinch the fourth seed and keep the Penguins in fifth.
The Bruins ended another disappointing season, their first under coach Dave Lewis. They lost their last six games and went 1-10-1 in their last 12. First-year general manager Peter Chiarelli, Ottawa's assistant GM last season, overhauled the Bruins roster, but they missed the playoffs for the second straight season and have won just one playoff series in 11 seasons.
With the score 2-2, Heatley's slap shot from the top of the left circle went between goalie Tim Thomas' right pad and the post with 5:15 gone in the second period.
Jason Spezza made it 4-2 at 8:52 of the period with his second goal of the game and 34th of the season when he redirected Christoph Schubert's shot from the left point.
Boston was 2-9 in its last 11 home games, giving fans little to cheer. One of the loudest reactions came with the score 4-2 when the scoreboard showed Boston College beating Michigan State 1-0 in the NCAA championship hockey game in St. Louis.
The fans did have more to cheer when the Bruins cut the lead to 4-3 with 3:42 gone in the third period on Petr Tenkrat's ninth goal on a power play.
But the Senators scored twice in the next six minutes - Daniel Alfredsson's 29th goal and Patrick Eaves' 14th. Alfredsson, who added two assists, scored with a two-man advantage when he fired a slap shot from the top of the left circle over Thomas' pad.
The Senators will be making their 10th straight playoff appearance, the longest current streak among Canadian teams. The could have clinched home-ice advantage on Thursday but they lost to Pittsburgh 3-2.
Boston struck early on Saturday with Marco Sturm's 27th goal with just 1:28 gone. Mike Comrie tied it two minutes later, but Petr Kalus restored Boston's lead less than three minutes later. Ottawa tied the game less than a minute later, with 6:50 gone in the game, on Spezza's first goal of the night.
Notes:The Bruins finished under .500 at home (18-19-4) for the third time in nine seasons. Before that stretch, they had gone 30 seasons without a losing record at home. ... Ottawa evened its season series with Boston 4-4. ... Senators goalie Ray Emery was 4-2 against the Bruins, including a 3-0 win in their previous game.