Harper and his group, including his wife and three former prime ministers, shuffled past Mandela’s body, which is lying in state at the Union Buildings in Pretoria, the seat of political power in South Africa.
"This is a profound time of sadness for us, and I know for many people," Harper said later, as he was joined by most of the Canadian delegation at the Canadian high commissioner's residence.
"With the passing of Nelson Mandela, freedom has lost a champion."
The coffin will rest for three days in an amphitheatre which bears the name of the anti-apartheid icon, who died last Thursday at the age of 95.
A state funeral for the former South African president, the first state funeral ever held in modern South Africa, is scheduled for Sunday.
In a frenzy of confusion that has marked events since Mandela's death, no foreign media were allowed into the amphitheatre where world leaders quickly filed past the coffin.
The mood in Pretoria turned sombre as the country mourned the loss of a leader affectionately known as Madiba. There was also anger over communications mixups that saw thousands of people show up in front of the capital buildings to wait for public viewings to begin, only to be told they would have to be bussed in from a university campus several kilometres away.
Still, throngs of people in the streets continued to celebrate Mandela’s legacy, singing, dancing and chanting, just as they did on Tuesday at a mass memorial in Johannesburg.
By mid-afternoon, however, the open-air celebrations were curtailed as the skies opened up with lightning, high winds and a torrential downpour.
Following the viewing, Harper appeared relaxed, even jovial, as he announced funding for new university scholarships in honour of Nelson Mandela.
The prime minister joked as he thanked former prime ministers Brian Mulroney, Jean Chretien and Kim Campbell for joining the delegation, which also included Joe Clark, who left after Tuesday’s memorial.
"There’s Chretien, Campbell, Mulroney and Harper on an airplane, and there are only three parachutes," Harper chuckled.
"But I won't try and finish the rest of the story."
Harper said he found the whole journey to remember Mandela "surreal" in that it had evolved into a historic gathering of a Who’s Who of Canada’s political elite.
The prime minister also mentioned _ after some encouragement from wife Laureen _ that Wednesday marked their 20th wedding anniversary.
Alberta Premier Alison Redford and former governor general Michaelle Jean also left the delegation early to attend other engagements.
But other notables remained, including former governor general Adrienne Clarkson, Opposition Leader Tom Mulcair, the premiers of Nova Scotia, the Yukon and the Northwest Territories, as well as two junior cabinet ministers, a handful of members of Parliament and Shawn Atleo, national chief of the Assembly of First Nations.
Flanked by this entourage, Harper announced new scholarships in Mandela's memory to benefit both Canadian and African students.
"Nelson Mandela believed that education is the foundation of democracy,'' Harper.
"He told us that nation-building and prosperity depend on the education of our future leaders.''
The Africa scholarships are aimed at helping early career public-sector professionals in Africa to study governance, public policy and administration.
The program will consider candidates from across Africa for one to two years of study in Canada, with special consideration given to female students.
Harper said the scholarships will help Africans gain the knowledge required to advance economic and social development in their home countries.
The Department of Foreign Affairs will contribute up to $5 million over five years toward the scholarships, to be matched by the MasterCard Foundation.
The Canadian scholarships will be open to as many as 20 Canadians pursuing master's or doctoral-level degrees in social sciences and humanities.
Their studies will focus on national unity, democracy, freedom and human rights, which Harper said Mandela had ''championed so tirelessly during his remarkable life.''
Up to 10 master's scholarships and up to 10 doctoral scholarships will be awarded for the first time in 2015, following a 2014 competition.
While the scholarships are new, the money for them is not. They will be financed through existing programs within the Canadian International Development Agency.
Harper concluded his remembrance of Mandela by taking a guided tour of the Apartheid Museum in Johannesburg.
He and the rest of the delegation are expected to return to Ottawa by late Thursday.
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