Baltimore (11-4) has won seven of nine.
The Red Sox, who have dealt with numerous injuries and illnesses, suffered another blow when second baseman Dustin Pedroia was forced to leave the game in the eighth when he was spiked in the left calf by Machado.
Bundy (3-1) was masterful for the second straight outing.
Five days after keeping Toronto scoreless through six innings, Bundy was equally effective against Boston. He allowed six hits with three strikeouts and one walk over seven-plus innings.
Christian Vasquez ended Bundy's night with a leadoff single in the eighth. Bundy became the third straight Orioles starter to pitch into the eighth inning, joining Ubaldo Jimenez and Wade Miley.
Donnie Hart struck out Andrew Benintendi looking in the eighth with runners on first and third to preserve the shutout. Brad Brach picked up his third save with a perfect ninth.
Machado had two hits, including his third home run of the season.
Left-hander Drew Pomeranz (1-1) had his second solid start against the Orioles this season. This time, however, he could not pick up the win.
Pomeranz allowed two runs on five hits with four strikeouts over 5 1/3 innings. Boston went 0 for 9 with runners in scoring position.
The Red Sox threatened in the second inning with one out and runners on the corners. However, Bundy escaped by getting Vazquez to hit into a 6-4-3 double play.
Baltimore took a 1-0 lead in the third on an RBI single by Adam Jones that scored Craig Gentry, who led off with a double and took third on a passed ball. Machado boosted the lead to 2-0 with a solo shot to center field in the fifth.
The Orioles helped out Bundy defensively by turning three double plays in the first three innings.
NOTES: Red Sox CF Jackie Bradley Jr. (right knee sprain) returned from the disabled list Friday for the series opener in Baltimore. To make room, OF/INF Brock Holt (vertigo) was placed on the 10-day DL. ... RHP Zach Britton's (left forearm strain) had an MRI on his left elbow and forearm Friday, but the results were not immediately available. However, Orioles manager Buck Showalter said Britton was feeling better and is lobbying to pitch again. ... Boston SS Xander Bogaerts (thumb) was out of the lineup Friday against Baltimore. Bogaerts injured the thumb Thursday against Toronto sliding headfirst into second base.