Chris Phillips also scored for Ottawa, winners of five straight road games and six of seven overall. The Senators have won the last two meetings against Boston after losing the first three this season.
The Senators didn't do anything fancy. They grabbed a lead and played well in front of Emery.
"It was nice. We've had struggles with Boston this season, but beat them the last two," Heatley said. "We need these points. They're big division games, especially before the break."
Emery felt his night was easier against Boston because of a defensive attitude this time.
"Sometimes that happens against certain teams. Sometimes you lose confidence against certain teams," Emery said. "The start of the season we'd get leads and try to win games 5-0 instead of 2-0."
It was just the second time Boston has been shutout this season; the other came in a 5-0 loss at Nashville on Dec. 30.
Hannu Toivonen, looking for victories in consecutive starts for the first time this season, stopped 36 shots for Boston.
Boston coach Dave Lewis was disappointed with his team's performance in front of Toivonen.
"We had no energy, no legs," Lewis said. "Guys tried. I've played in games like this. You try everything to turn it around, but nothing works - except for Hannu. Hannu was the bright star of the game."
The Bruins were held to their lowest shot total this season.
"We have to chalk it up as one of those games where we couldn't get anything going," Boston wing Mark Mowers said.
Heatley's second goal was a shorthanded, empty-netter in the closing seconds. Like they did most of the night, the Senators played well while they were down two skaters in the final minute.
"Defensively it was just an excellent effort," Ottawa coach Bryan Murray said. "Our forwards came back and really helped out, and Ray made a couple of key saves."
Ottawa grabbed a 1-0 lead on Phillips' goal 17:16 into the opening period when he collected the rebound of Peter Schaefer's shot at the bottom of the left circle and slipped a shot past Toivonen.
The Senators made it 2-0 on Heatley's power-play goal 15:03 into the second period. Tom Preissing fired a shot from the point that Toivonen stopped, but the puck slipped behind him and Heatley backhanded it into the open net.
Ottawa had an excellent chance for more scoring when it was awarded a 5-on-3 advantage late in the second period. Boston defenseman Andrew Alberts was given a 5-minute major for boarding and Marc Savard was called for unsportsmanlike conduct.
The Senators had another two-man advantage midway into the third, but Toivonen kept them scoreless with a couple of good stops on shots from close.
The Senators kept the Bruins' offense in check for most of the first two periods, owning a 26-12 shot advantage. Boston's first decent scoring chance didn't come until Savard broke in on a partial break two minutes into the second, but Emery handled the shot easily.
- Boston RW Glen Murray's next assist will be the 300th of his career.
- Ottawa D Christoph Schubert was whistled for diving while attempting to draw a penalty late in the second period.
- The teams meet again in Ottawa after the All-Star break next Saturday.