The Luxembourgish politician concludes his time as one of the European Union's (EU) most senior figures, making way for German conservative Ursula von der Leyen who was voted in to replace him, Efe news reported.
"Take care of Europe. And fight with all your force against stupid and blinkered nationalism. Long-live Europe," Juncker said, concluding what is likely his final address to the European Parliament as Commission chief.
The 64-year-old took a look back at the milestones of his five-year mandate at the helm of the EU's executive arm as well as the disappointments along the way, including the failure to agree on arrangements with Switzerland and the lack of progress on Cyprus' reunification.
He made no reference to Brexit in his farewell speech, but earlier described it as a waste of time and energy.
The UK's Parliament is due to vote on Prime Minister Boris Johnson's deal later in the day.
Going over the positives, Juncker said he had presided over 25 consecutive quarters of economic growth.
He also mentioned Greece's bailout following the economic crisis in 2008/9.
Juncker said he regretted that "many countries" had failed to abide by the EU's policy on accepting migrants, a crisis that occupied much of his time in office.
And he lamented commercial tensions that have rocked the global economy for part of his tenure.
He said that during a meeting with US President Donald Trump, slated in a bid to avoid a looming trade war with China in 2018, he explained that the Commission represented the unified commercial stance of 28 member nations.
"I think that impressed him a lot," he said.
Juncker said he brought his mandate to a close "neither excessively cheerful nor terribly disappointed".
European People's Party group leader Manfred Weber praised the outgoing Commission's chief ability to find consensus.
"Not even Donald Trump managed to resist your way of making compromises."
The leader of the Socialist bloc in the European Parliament, Spaniard Iratxe García, lamented that Juncker's "new beginning" in 2014 had only been half completed.
( With inputs from IANS )