Matheson, a former MP and Second World War veteran, died Friday in Kingston, Ont.
He was often referred to as the father of Canada's now-familiar Maple Leaf flag.
Matheson lead a multi-party committee that chose the new flag to replace the old Red Ensign in 1965.
The Sunday night tweet from Harper's account also pointed out that Matheson was instrumental in the creation of the Order of Canada.
Matheson was first elected as a Liberal MP for the Ontario riding of Leeds in a 1961 by-election, and was re-elected three times before being defeated in 1968.