"I am convinced that Italy will be able to play an important role in addressing these truly European challenges and will live up to its responsibilities as a founding member of our Union," Juncker tweeted.
He attached his letter of congratulation to Giuseppe Conte, who led the previous populist-far-right government, on his re-appointment as Premier.
"The formation of the new government you lead comes at a crucial time for our Union that needs a renewed commitment from all member states....the challenges we face - from migration to ensuring sustainable economic development and the security of our citizens - are not for nations to tackle alone but all together," read the letter.
"Thanks to your leadership and the support of our government, I am convinced that Italy will be able to play a leading role in tackling these essential European challenges and will be equal to its responsibilities as a founding EU member state....I wish you the best of luck."
Brussels had frequently tense relations with Italy's previous coalition government between the grassroots 5-Star Movement and the far-right, eurosceptic League party. That administration, also led by Conte, constantly railed against EU budget and migration rules during its 14 months in power.
The unlikely tie-up with the pro-European Democratic Party (PD) comes after League party leader Matteo Salvini pulled the plug on the fractious coalition with 5-Star last month in the vain hope of triggering and winning snap polls.
Markets have rallied at the new government in which the PD has taken charge of the economy and European affairs ministries. Former PD premier Paolo Gentiloni has been named as Italy's next EU Commissioner, a further appointment seen as smoothing ties with Brussels.
( With inputs from IANS )