After the event at the European Parliament, he will be buried in the German town of Speyer later.
Former German Chancellor Helmut Kohl sits next to Christian Democrat party (CDU) leader Angela Merkel during celebrations to mark the 10th anniversary of German unification in Berlin on September 27, 2000.
"Helmut Kohl gave us the chance to be involved in something bigger than ourselves", said former U.S. President Bill Clinton, citing Kohl's willingness to put global cooperation before national interests at key moments in history.
Mr Clinton also cited Mr Kohl's willingness to put global co-operation before national interests.
Junker said the ceremony at the European Parliament's seat in the French city of Strasbourg, close to the border with Germany, was the choice of Kohl himself.
Walter Kohl has described the European Parliament commemoration as "unworthy" in an interview with German newspaper Die Zeit.
"I express deep sorrow on the passing of former German Chancellor Helmut Kohl", he said.
Kohl died on June 16 at age 87 and his coffin draped with the flag of the European Union was placed in the chamber of the EU legislature in tribute to the leader known as the father of German reunification.
Kohl married Kohl-Richter, 34 years her husband's junior, when he was 78.
The funeral plans for Germany's longest serving post-war leader, in office from 1982-98, include a European ceremony in Strasbourg on July 1.
Netanyahu shook hands briefly with several world leaders and prominent figures, including French President Emmanuel Macron, German Chancellor Angela Merkel, British Prime Minister Theresa May, and former United States president Bill Clinton.
Kohl's casket was flown by helicopter across the Rhine from Strasbourg to his hometown of Ludwigshafen, where his body was later carried in procession before being transported by riverboat to nearby Speyer.
That decision has been criticised by Mr Kohl's son by his first wife, Walter Kohl, who wanted a farewell ceremony near the Brandenburg Gate in the German capital Berlin, near the site of the former Berlin Wall.
Kohl is widely regarded as having skillfully overcome the fears of Germany's neighbors when an end to the country's decades-long division into a communist east and a democratic west first became a realistic possibility in the late 1980s.