Tyrell Goulbourne also scored for Kelowna (9-6-2), which handed Kamloops its first regulation-time loss of the season.
Rockets goaltender Jordon Cooke stopped 19 shots for his second shutout of the season.
Kelowna hadn't played since Sunday and was the fresher of the two clubs, especially in the third period when Fowlie scored both of his goals.
Cole Cheveldave made 23 stops for the Blazers (16-1-1), who were playing their fifth game in seven days.
The loss was also Kamloops' first shutout defeat of the season. The Blazers' last loss was 4-3 in a shootout to Victoria on Sept. 28.