The two leaders embraced at the unveiling of a commemorative plaque at the site of the railway carriage where military leaders signed a ceasefire on 11 November 1918.
Following the laying of wreath and a minute’s silence, Mr Macron and Ms Merkel entered a replica of the carriage to sign a book of remembrance.
The current leaders of France and Germany have been keen to demonstrate the strength of the alliance that now unites the formerly warring nations.
The Armistice deal came into force on the 11th hour of the 11th day of the 11th month of 1918, ending four years of fighting which saw the death of almost 10 million soldiers.
Dozens of world leaders have been arriving in France ahead of the key commemorations set to take place to mark Armistice Day on Sunday.
Some politicians have visited military cemeteries where their nation’s soldiers fell 100 years ago.
But US President Donald Trump cancelled a trip to the battleground of Belleau Wood scheduled for Saturday because of the rain.
The decision regarding the bad weather followed an awkward meeting with Mr Macron at the Elysée Palace early on Saturday, as both leaders tried to play down a spat over NATO security.
Belleau Wood, 50 miles east of Paris, was where US troops had their breakthrough battle shortly after entering the war in 1917, stopping a planned German push for Paris.
Instead of travelling to the Aisne-Marne American cemetery, Mr Trump tweeted: “Is there anything better to celebrate than the end of a war, in particular that one, which was one of the bloodiest and worst of all time?”
Earlier on Saturday, Prime Minister Theresa May paid respects to the first and last British soldier killed in the First World War.
At a ceremony at the Saint-Symphorien cemetery in Mons, Belgium, Ms May lay wreaths at the graves of Private John Parr, killed 21 August 1914 in the woods south of Brussels, and Private George Ellison, who was shot and killed in a Belgian pasture on 11 November 1918 – the war’s last day.
Canadian Prime Minister Justin Trudeau went to Vimy Ridge at dawn on Saturday, the site where Canadian forces defeated German opposition against the odds.
Mr Trudeau said everything his country had achieved in the past century was “a history built on your sacrifice. You stand for the values on which Canada was built.”
On Friday, the German chancellor made a speech at a Berlin synagogue to mark the 80th anniversary of Kristallnacht – the Nazi attacks on the Jewish people, which refers to the broken glass that littered streets outside synagogues, shops and homes.
“Jewish life is blossoming again in Germany – an unexpected gift to us after the Shoah,” said Ms Merkel, using the Hebrew word for the Holocaust. “But we are also witnessing a worrying antisemitism that threatens Jewish life in our country.”
On Sunday, more than 60 international leaders will mark the centennial during the day’s key event at the Tomb of the Unknown Soldier underneath the Arc de Triomphe in central Paris.
In another show of reconciliation between France and Germany, Mr Macron and Ms Merkel are expected to open an international peace forum in Paris with UN secretary-general Antonio Guterres.