The Torino 2006 Olympic champion delivered an outstanding performance, posting the highest turns score and racing down the Calgary course in 21.90 seconds, half a second ahead of any of the other 16 finalists.
He was also rated third for his jumps.
Begg-Smith collected 25.25 points from the judges, 0.55 ahead of defending World Cup champion Alexandre Bilodeau of Canada.
Russia's Alexandr Smyshlyaev took the bronze on 24.42 points.
"That was a great performance today," said Olympic Winter Institute CEO Geoff Lipshut.
"He had fantastic speed and to be able to come back to top line like this less than 12 months after major surgery is just a wonderful effort."
The back-to back victories now have the AIS skier at the top of the world rankings, a position he occupied for three consecutive years before injuring his knee in January 2009.
Begg-Smith has amassed 295 points from the season's four events, 14 points ahead of Sweden's Jesper Bjoernlund.
Bilodeau is in third position on 205 points.
Begg-Smith's AIS team-mate Ramone Cooper struggled with some lower leg soreness and placed 27th while World Cup rookie Sam Hall finished in 32nd position.