The Prime Minister insisted “it was an honour” to work with the German Chancellor. Ms Merkel’s 16-year reign as Chancellor came to an end on Wednesday.
Her departure from the front line has marked the end of an era in German politics.
Mr Johnson described the outgoing leader as a “titan of international diplomacy”.
He added that Ms Merkel may no longer hold the top job but that her long time in office will continue to shape German and wider politics.
The Prime Minister, quoted in Bild, said: “Compared with any other European leader in this century, she has certainly made the greatest contribution on the international stage, and I am convinced that her legacy will shape future generations.”
He remembered fondly the G7 meeting held in Cornwall in June this year, attended by numerous world leaders, including Ms Merkel.
He said: “It was an honour to welcome her to her last G7 meeting in the UK this year.
“Her knowledge of topics such as global health, climate change and development cooperation was greatly appreciated by all of us and will now be profoundly missed.”
The relationship between the German press and the UK appears, upon Ms Merkel’s departure from office, to be a little more frosty.
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But Mr Johnson has insisted that, despite the political differences between the two nations, Ms Merkel will be remembered as a sturdy leader for whom the “undivided attention” of those listening to her advice was deserved.
During her 16 years in office, she visited Britain more than 20 times.
Ms Merkel’s successor is Olaf Scholz of the German Social Democratic Party (SPD).
Other world leaders have bid their farewell to Ms Merkel.
US President Joe Biden, who is also known to have had his disagreements with the German Chancellor, said during a press conference: “On a personal note, I must tell you I will miss seeing you at our summits.”
Additional reporting by Monika Pallenberg.