McEwen stole one in the seventh and added another point in the eighth for the victory at the Essar Centre in Jacobs' hometown.
"I thought we recovered quick from a few misses that I made. The guys really supported me to give me that chance to mentally come back," said McEwen. "I was pretty proud of the team for how consistent they were and propping me up a little bit for the first half of the game."
With the win, the Winnipeg skip moves past Jacobs and into top spot on the World Curling Tour's Order of Merit.
"Unfortunately, we didn't bring our best effort to the ice today and we didn't get any breaks, and you lose as a result of that sometimes," said Jacobs. "It was a really fun event for us. We would have loved to win it for the Soo, but we just didn't have it today."
The National is the second of five Grand Slam of Curling events this season.
McEwen reached the final at the Masters earlier this month but lost to 2006 Olympic champion Brad Gushue of St. John's.
The next Grand Slam stop is the Dec. 9-14 Canadian Open at Gallagher Centre in Yorkton, Sask.