The Northeast Division rivals meet again Tuesday at the ACC.
Marc Savard and Petr Tenkrat also scored for the Bruins (10-9-2), who have taken two of three against the Leafs this season.
Mats Sundin, in his return after a seven-game absence, scored the lone goal for the Leafs (13-8-4), who were dominating the Bruins in the third period before Boyes, a former prospect, ended their chances.
Andrew Raycroft was solid in net for the Leafs, stopping 22 shots, limiting what could have been a worse result.
Tim Thomas stopped 27 shots for the win in goal for Boston, helping the Bruins win for the sixth time in the last eight games.
Sundin, who recovered from an elbow injury, started the game between John Pohl and Chad Kilger but by the second period had been reunited with Nik Antropov and Alexei Ponikarovsky.
It is Sundin who finally solved Thomas when he banked a rebound behind him during a made scramble on a Leafs power play at 12:04 of the third period, the captain’s ninth goal this season.
The Leafs then pressured in waves but couldn’t get the equalizer. Boyes, parked alone in front, slipped a shot between Raycroft legs to quiet the crowd of 19,473.
The Bruins came roaring out the gates and dominated the Leafs for the opening seven minutes and it produced a goal at 6:04 when newly acquired Stanislav Chistov fed a pretty pass to an onrushing Tankrat who beat Raycroft top corner on the glove side from the slot.
Savard made it 2-0 eight minutes later during a Boston power-play when he one-timed a wrist shot, again glove-side and top corner on Raycroft.
Late in the period Darcy Tucker ran big Zdeno Chara, which led to a centre-ice tussle between Tucker and Bruins blue-liner Paul Mara.
The Leafs lost defenceman Pavel Kubina halfway through the second period when he took a puck in the face.
Jeff O’Neill, left alone in front, had a glorious chance to open the scoring for Toronto but was stoned by the Bruins goalie with nine minutes to play in the middle period.
Notes: With Sundin activated from injured reserve, the Leafs will place rookie defenceman Jay Harrison on 48-hour waivers at noon ET Sunday. If he’s unclaimed by another team by noon ET Tuesday, he’ll report to the AHL Marlies … The Bruins may possibly recall goalie Hannu Toivonen from AHL Providence in time for Tuesday’s rematch. Goalie Brian Finley remains day to day with a groin problem so Phil Sauve dressed as the backup to Thomas for the second straight game … Bruins defencemen Nathan Dempsey and Milan Jurcina were healthy scratches for Boston while Toronto didn’t dress blue-liner Brendan Bell and forward Aleksander Suglobov … The Leafs went 4-2-1 in Sundin’s absence.