She was due to arrive in Buenos Aires at around 2100 GMT - without her husband Joachim Sauer, who after the plane troubles opted to skip the event.
At a Friday press conference, an Air Force spokesman ruled out foul play as the cause of the malfunction, despite early reports the aircraft may have been tampered with.
Merkel and other passengers initially remained on board the aircraft, called "Konrad Adenauer", as mechanics inspected its brakes and several fire engines waited nearby, according to a Reuters reporter on board.
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Around an hour into the trip from Berlin, the captain told passengers he had chose to land at Cologne-Bonn airport in northwestern Germany after the "malfunction of several electronic systems".
The plane had suffered a complete breakdown of the on-board communication system, a problem described as extremely rare, which forced the pilot to communicate via a satellite phone instead.
Photos from the scene show firefighting vehicles with their lights flashing waiting for the malfunctioning plane at the airport. "We will not be proceeding today", she told AFP.
It's not the first time for German officials were left stranded. Scholz experienced a mishap last month returning from Bali, Indonesia, when rodent damage incapacitated the same government plane. Merkel is expected to meet Russian President Vladimir Putin to discuss Syria and Ukraine, including the recent incident in the Kerch Strait.