The US president returned the compliment, tweeting that it was a "great honour" to attend the "magnificent" parade.
Macron invited Trump to be the guest of honor at Friday's celebration, which also commemorates the 100th anniversary of the USA entry into World War I.
With his free hand, Macron rather awkwardly points to something for Trump to look at, all the while continuing with the handshake.
The interaction remained friendly, despite tugging on occasions from both Mr Macron and the US President.
Mr Trump and Mr Macron already have a slightly rocky relationship, as the French President has publically criticised Trump's decision to pull the USA out of the Paris climate change accord.
Macron was due to fly to Nice to commemorate the victims after bidding Trump farewell in Paris.
The conversation was initially off the record, meaning reporters could not make public what Trump said. They then engaged in an interminable hand clasp before Mr Trump was whisked away in his motorcade.
Trump's visit to Paris has drawn global attention. The iconic Champs-Elysees avenue where the parade took place was the target of two recent extremist attacks.
Macron said there was still "disagreement" on climate and no breakthrough on commerce, but he said that he and Trump saw eye to eye on the importance of "fair, free trade".
The warm body language between him and Macron seemed at odds with broader concerns about the transatlantic relationship since Trump's election victory in November previous year.
Trump pointed to a cease-fire the USA and Russia negotiated in a region in Syria and said it was a result of having communication with Russian President Vladimir Putin. Thursday saw a full military review and a tour of Napoleon's tomb at Les Invalides before a haute dining experience on the second landing of the Eiffel Tower.
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