The two leaders met for close to an hour in a discussion that lasted twice as long as had been originally expected.
"Obviously, Mr Putin has his own perspective — but I urge Russia to play a more positive role than it's been playing," Harper said after the meeting ended.
The Prime Minister would not say if he made any progress in his efforts to sway Putin.
Although there are a number of other issues on the table in the discussions between Canada and Russia, Canada's ambassador to Russia says the entire relationship is in a holding pattern because of Syria.
Moscow blocking UN resolution
Russia is blocking any United Nations resolution that would bring military sanctions against the Syrian regime for its brutal crackdown against armed opposition groups.
In an interview on Friday, Putin said Western countries still haven't finished what they started in Afghanistan or Iraq — so he doesn't see what invading Syria would accomplish.
A senior government official who was in the room for Saturday's meeting described the spirited exchange on Syria to The Canadian Press on the condition of anonymity.
Putin told Harper that Russia is not a friend of the Assad regime; Russia just wants stability and a diplomatic solution, the official said, adding that Harper reiterated Canada's long-standing position that a diplomatic solution is the best option.
In Syria, President Bashar Assad has battled an 18-month uprising that has left at least 23,000 his citizens dead.