Kieran McGachie headed the ball home for the hosts to sicken the Motherwell outfit, who had netted an early second half headed equaliser by Marc Kelly through after Bonnyrigg had taken a 10th minute lead from a debatable Lee Currie penalty awarded for a challenge by Zac Butterworth.
“Bonnyrigg must have had about 15 to 20 corner kicks,” Braves manager Ricky Waddell told the Times and Speaker.
“And they thrive on that. I had warned my players about giving away too many corner kicks but it’s very difficult because Bonnyrigg will play it into the corners, chase it down and play for corners a lot of the time.
"We were great in defending corners until the very last one of the game.
“Big McGachie’s peeled off at the back post and scored. I’m gutted for the guys because they’d put so much into it.
"The manner of the winning goal was a bit of a killer.”
Waddell admitted that Braves had been second best for much of the opening 45 minutes before improving after a half-time pep talk.
"I didn’t think we were particularly great in the first half but we were so much better in the second half,” he added.
"We defended really well right through the game. We were missing a few as well, with a couple of Covid cases and quite a few injuries.
"We had a young team against a very experienced team and that’s no excuse because I would loved to have got the point.
"I don’t know if we did enough to merit the three points but we certainly had our chances as well.”
Braves, 11th in the table with 28 points from 22 games, host Broomhill in the league this Saturday with kick-off at 3pm.
"Broomhill have been up and down,” Waddell said. “We really want to come out the traps well.
"We’ve got a resilience about us at the moment which is good. We’re starting to get boys back from injury as well.”