After 50 minutes of play, Brandon Goodwin put the Bulldogs up 1-0 off a pass from Tyler McClinton, giving him 11 goals in the last four games.
"He scored on a great hustle play," Sikeston coach Doyle Noe said. "The other kids are really feeding off him right now."
At the 60th minute, Josh Bill scored on a pass from Tyler Neal for what ended up being the game winner after Carbondale scored in the 70th minute.
The win moved the Bulldogs to 14-4 on the year, just one win shy of tying the school record they set last season.
On the junior varsity side, Sikeston shutout Carbondale 5-0. Zach Harrison had a pair of goals with Audi Hay, Patrick Smith and Caleb Hampton collecting one each.
Sikeston will host Cape Central on Thursday with junior varsity action starting at 5 p.m.