During two days of closed-door G7 leaders' talks in Brussels, Harper and Obama were firmly aligned against the plans of several fellow leaders to sit down with Putin, a source close to the talks said Thursday.
Harper has consistently urged other countries and Canadian businesses to actively isolate Putin on the world stage.
France invited Putin to Friday's commemoration in Normandy to mark the 70th anniversary of the D-Day invasion, which began the liberation of Europe from the Nazis.
Putin's imminent arrival has exposed cracks in an otherwise united G7 front that produced a public declaration denouncing his annexation of Crimea and provocations in eastern Ukraine.
British Prime Minister David Cameron, French President Francois Hollande and German Chancellor Angela Merkel are to meet Putin this week and engage him on the Ukraine crisis.
Hollande and Cameron both were to meet Putin on Thursday in Paris, according to Russia's ITAR-TASS news agency. His meeting with Merkel is to come in the French resort of Deauville on Friday.
Hollande has mused that the Normandy setting might be conducive to a positive meeting between Putin and Ukraine president-elect Petrol Poroshenko on Friday.
Behind closed doors, Harper and Obama were united in making it "crystal clear" that they had no intention of meeting Putin, said the source, speaking on condition of anonymity about matters that hadn't been publicly disclosed.
Harper and Obama also expressed the view that it was "not ideal" for other leaders to meet him, but if they did, the main message should be a direct, agreed denunciation of Putin's actions on behalf the entire G7, the source said.
"The fundamental point is that this was driven hard by the prime minister and President Obama."
Harper alluded to those discussions during his closing news conference in Brussels on Thursday, after which he departed for France in advance of the D-Day anniversary.
Harper said he and his fellow G7 leaders had "a very detailed discussion of the messages that need to be sent to Mr. Putin about ending illegal occupations, about ending provocative actions, ending the supporting of violent actions in eastern Ukraine and the necessity of the G7 taking further actions if those things are not done."
G7 leaders are united in denouncing Putin's actions in the Ukraine crisis, Harper said. "All of our allies are agreed that those messages and only those messages will be the things that are communicated to Mr. Putin."
The prime minister flies to Kyiv on Saturday for the official swearing-in of Poroshenko, a billionaire candy maker.
Harper, meanwhile, said that Putin should be allowed to attend Friday's D-Day ceremonies because the Soviet Union played a major role in defeating Nazi Germany.
"Obviously whatever contemporary difficulties we have with the current regime there, and they're obviously immense, I don't think we want to in any way diminish the Soviet and Russian contribution to the war effort, which was obviously enormous at the time," he said.
The West's general strategy is to politically isolate the Russian leader over the Ukraine crisis.
In their communique issued late Wednesday, the G7 leaders did not impose any additional sanctions but reserved the right to do so.
The group also called on Putin to co-operate with Ukraine's new government.
But rifts in the G7 emerged as the summit ended.
In his final news conference, Obama said he is concerned that France plans to proceed with a contract to build warships for Russia.
France plans to go ahead with the $1.6-billion deal, which will include training Russian sailors, as part of a three-year contract.
Obama said he understands the deal is important for jobs in France, but said it "would have been preferable to press the pause button" on the deal.
Hollande stressed the unity of the G7 on Thursday, saying, "the important thing is we have the same language, the same arguments on Ukraine all together."