The prime minister and Gen. Tom Lawson, Canada's chief of the defence staff, sang the national anthem while standing on the field before a game between the Ottawa Redblacks and the Montreal Alouettes.
A massive Canadian flag was unfurled over the field during the anthem and players from both CFL teams helped hold it in place.
The ceremony was dedicated to Cpl. Nathan Cirillo and Warrant Officer Patrice Vincent.
Vincent was killed and another soldier injured Monday when they were struck by a car driven by a man with jihadist sympathies in St-Jean-sur-Richelieu, Que. Cirillo was shot two days later at the National War Memorial in Ottawa before the gunman stormed into Parliament's Centre Block.
There was a significant security presence at the football game as two armed soldiers in full combat gear stood watch nearby during Harper's appearance.
Fans stood and applauded for Harper and Lawson as they left the field.
On Saturday night, the NHL's Ottawa Senators, Montreal Canadiens and Toronto Maple Leafs are scheduled to hold co-ordinated tributes to Cirillo and Vincent.