A late goal from Ethan Whiley ended Boomers' winning run and lifted Wangaratta back among the league's front-runners.
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Whiley scored with a header, seven minutes from time, to hand the Devils a precious 2-1 win after Andrew Grove's penalty had earlier cancelled out a Dan Kelly opener.
That made it three league wins in a row for Wangaratta, who are now one of six sides covered by a single point at the top of Division 1.
"It's a great feeling when you beat Boomers," coach Daniel Vasilevski said. "They're a top side and we knew that if we could beat them, we'd go equal points with them and keep in touch with the top two or three.
"We were a little bit under-strength coming but we had a game plan and we had a couple of young boys come in who stuck to it and we executed it well."
Boomers livewire Kye Halloway created an early chance out of nothing when his curling shot forced a fine fingertip save from Tommy McCarron.
At the other end, Kelly missed with a free header from a corner and Adam Burchell's snap shot was brilliantly turned onto the post by Seb Turner.
Wangaratta took a 20th-minute lead when Burchell latched onto a throw-in, spun his man and squared to give Kelly a simple finish.
But when Du Phan was barged in the back, Grove found the bottom left-hand corner from the spot to send the sides in level.
After the break, Boomers took control and it seemed only a matter of time before the visitors hit the front.
Everything was going through Grove, who flashed two shots across the face of goal with the home side on the ropes.
However, a Kelly strike which rattled the post seemed to galvanise Wangaratta and Burchell had a low shot kept out by Turner, who then adjusted well to grab Jordan Vellien's deflected effort which threatened to catch him out.
The game seemed destined for a draw until Burchell swung a high free-kick into the box and Whiley showed the greatest desire to score from close-range.
"We were the better team but we didn't convert our opportunities," Grove said.
"It was a frustrating day and the goal we conceded was soft at the back post but if you put them away, you win, it's as simple as that.
"Wangaratta have always been like that. They've always managed to get the goals when they matter.
"Even if they're having a off-day, they still manage to find a way to win. That's what good teams do and that's what we need to find.
"We need to find that killer instinct in front of goal."
Vasilevski hailed the character of his new-look side in pushing for the late winner.
"I thought we started better but when we scored our first goal, we took our foot off the pedal," he said.
"We let them control the midfield, they started winning the second ball, got 'Grovesy' and Kye on the ball and they're dangerous when those players get on the ball.
"In the second half, we thought 'we've got this', they started to drop off a bit and we could see they were starting to get a bit tired.
"We dug really deep to grind out the result and that was the most important thing to see.
"Playing at home, you can get that extra 10 or 15 percent and it came with a reward at the end.
"Ethan is such a good player when he's going forward.
"For him to play a full game and pop up at the end and score is a big confidence-booster for him.
"He usually gives us 45, 60 or 70 minutes but now he's played 90 and scored at the end."
Elsehwere, Melrose thrashed Wodonga Diamonds 7-0 and Cobram were 3-1 winners over Twin City, while Myrtleford beat St Pats 1-0 at Alexandra Park.
Albury Hotspurs and Albury City played out a 1-1 draw.
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