Sundin returned to the lineup and scored a power-play goal in the third period, but the Maple Leafs looked sluggish in the first two periods -- one night after routing Washington 7-1 in their biggest offensive output of the season.
"We had an easier night mentally last night in Washington and in the first period maybe we thought it would be easier," Toronto's Darcy Tucker said. "That's just not acceptable in our building."
Sundin, who missed three weeks with an elbow injury, spoiled Thomas' shutout bid at 12:04 of the third.
But Boyes, a former Leaf, gave Boston an insurance goal at 15:44 by redirecting Patrice Bergeron's pass from behind the net.
The Bruins, who are in last place in the Northeast Division, rebounded after losing 5-1 to Carolina on Friday. Boston coach Dave Lewis complained about their effort after the loss, but said Thomas was solid and didn't deserve to face the barrage of shots.
"Timmy stood tall and made some awesome saves," Boston captain Zdeno Chara said. "Last night we were flat. We didn't play well, simple as that and we all knew that. We wanted to come back hard and regroup."
Thomas said it was a big win.
"It's important to start winning games anywhere, but in the division it's even bigger," Thomas said. "Toronto was 10 points ahead of us in the standings going into tonight's game so these are the kind of four-point swings that are important."
The teams meet again in Toronto on Tuesday night.
Sundin didn't think his team needed to adjust with him back.
"Boston had more energy than us, that's for sure," Sundin said. "We didn't have a very good game. Was it because I played? I don't know. I'm not going to say that."
After a Toronto turnover by the blue line, Chara skated in on a 3-on-2 before Stanislav Chistov made a nice pass to a trailing Tenkrat, whose wrist shot beat Raycroft to his glove side at 6:04 of the first.
Savard made it 2-0 with a one-timer on the power play at 14:06 of the first. Bergeron and Chara assisted.
Toronto's John Pohl hit the post with a shot in the second, and the Leafs didn't have that many chances after that.
Boston's Paul Mara received a minor penalty with less than 10 minutes left in the third. After a shot and a scramble in front of Thomas, Sundin pushed the puck over the goal line to cut it to 2-1.
Thomas made a nice pad save on Pohl with less than five minutes left.
Some fans booed as the final buzzer sounded.
- After Toronto's Tucker nailed Chara into the boards with a check in the first period, a couple of Bruins went after Tucker, including Mara -- who started throwing punches as soon as he got to Tucker. Mara received a major penalty for fighting, a minor for instigating and a 10-minute misconduct.