The world champion American, pushed by Steven Langton, was too fast for World Championships silver medallist Lyndon Rush, who had to settle for second.
Canadian Rush and his partner Lascelles Brown came in 0.04 seconds behind Holcomb while there was a tie for third.
Germany's junior world champion Francesco Friedrich,with Jannis Baecker, and Russian duo Alexsandr Zubkov and Dmitry Trunenkov both clocked the same time, 0.34 seconds back.
The result means Holcomb extended his overall lead at the top of the World Cup standings, and his three wins from three events - in Park City, Lake Placid and now Whislter - leaves him on 675 points.
Friedrich is second on 600, while Cory Butner, who could only manage a 10th-place finish in Whislter, is third with 564.
British duo John James Jackson and John Baines came in 15th.