Phil Kessel also scored for Boston, which also drew even with Ottawa for sixth overall in the Eastern Conference with 94 points.
The Senators completed their regular season schedule, clinching a playoff spot midway through the third period when Florida beat Carolina 4-3. The result was announced to the sold-out Scotiabank Place crowd during a stoppage in play with 1:35 remaining, drawing a huge cheer.
The Bruins close the regular season Saturday night against Buffalo.
Chara gave Boston a 1-0 lead 6:39 into the second when he sent a slap shot past Martin Gerber from the top of the left faceoff circle for his 17th goal.
Kessel made it 2-0 with his 19th goal 4:21 into the third.
Despite trailing by two goals, Ottawa got good news with about 13 minutes remaining in the third with the result out of Raleigh which assured the Senators of an 11th straight playoff appearance.
Antoine Vermette, who scored his first career hat trick one night earlier, scored 11:46 into the third, ending Thomas' shutout streak against Ottawa at 180 minutes, 10 seconds. Thomas stopped 17 shots, improving to 4-0-1 in his last five starts against the Senators.
Ottawa, which got off to an NHL record 15-2 start after making its first modern appearance in the Stanley Cup finals, came perilously close to missing the playoffs for the first time since 1995-96.
Captain Daniel Alfredsson and center Mike Fisher were both injured in Thursday's crucial 8-2 win in Toronto and the team announced earlier Friday that both players will be sidelined "for weeks".
Notes@: The crowd of 20,232 was the Senators' 34th consecutive sellout and helped the team set a new single season attendance record. Ottawa's total attendance of 812,665
- an average of 19,821 per game - included 38 sellouts in 41 games at Scotiabank Place and topped the previous franchise record of 798,453 set in 2005-06. ... The Senators recalled LW Nick Foligno from Binghamton of the AHL.
