The bromance between the two EU chiefs came to an end after Mr Schulz was succeeded today by Italian Antonio Tajani.
And the European Commission President Juncker said: “I won’t hide it [I wish he was not going.]"
The EU leader struck a more moderate tone than last year when he had threatened to resign unless Mr Schulz remained parliament president.
European Commission President Jean-Claude Juncker embraces Martin Schulz
Schulz: Georgia has Europe's support in face of Russian threat
Corbyn will push for full access to the European single market
Schulz: Verhofstadt won't stand as European Parliament president
He said he could not “guarantee that I will remain president of the Commission” if Schulz is replaced by a conservative president he said in a closed door meeting.
However, the incoming parliament president, Mr Tajani, is also a close friend of Mr Juncker.
Mr Juncker said: “Seeing my friend 'Tonio' succeeding him fills my heart with joy.”
Mr Juncker leads the EPP, which also hold the presidency for the European Council
Mr Tajani, is the 29th president of the European Parliament.
The 63-year-old is a former spokesman for Italy’s controversial former prime minister Silvio Berlusconi and he was all his country’s ex-European commissioner.
Before his election as President last night, Mr Tajani served as one of the 14 Vice Presidents of the European Parliament.
Mr Schulz was succeeded today by Italian Antonio Tajani
Get Quotes on Home Insurance
The Italian forged an alliance with his centre-right European People’s Party (EPP) group and the Alliance of Liberals and Democrats for Europe to win.
He got 351 votes against another Italian Gianni Patella who got 282 in a fourth-round run-off.
Mr Juncker leads the EPP, which also hold the presidency for the European Council.
The funniest EU memes
Tue, June 28, 2016
Here are the funniest EU memes on the internet.
1 of 16
Jean-Claude Juncker: Marine Le Pen will not be President
Jean-Claude Juncker greets team by kissing and slapping
Jean-Claude Juncker: Malta will play 'pivotal' role in Europe