Prodi's Union coalition won the majority of seats in the lower house Chamber of Deputies by 24,755 votes, according to final results confirmed by the Supreme Court on Wednesday.
"Sooner or later they will recognise how things are, and since we are patient we will continue to be so," said the mild-mannered Prodi, 66, a stark contrast to the flamboyant Berlusconi, Italy's prime minister and richest man.
Prodi said he has "been working the past few days on the government's agenda".
Berlusconi has remained defiant since the results of the
April 9-10 election - one of the closest in Italian history - showed he had lost control of parliament.
For days, he alleged irregularities and at one point he even spoke of fraud, only to quickly retract.
He has said that the razor-thin margin of Prodi's victory required thorough checks and contended the vote of Italians abroad was marred by irregularities.
Berlusconi's proposal of a grand
coalition cabinet was dismissed
Berlusconi even raised the possibility of "a grand coalition" government, but the proposal was dismissed by Prodi and other centre-left leaders.
Although Berlusconi and some of his inner circle persisted in challenging the outcome of the vote, many in the centre-right looked forward instead to fighting Prodi from the opposition benches.
Writing in the pro-Berlusconi Il Giornale newspaper, a senator from Berlusconi's Forza Italia party, still Italy's largest, called Prodi's win a "pyrrhic victory" by an unwieldy coalition made up of moderate Catholics, liberals and Communists.
"The flimsiness of his majority will send everyone back to the polls very soon," Paolo Guzzanti said.
Official confirmation of the Senate vote, which Prodi's coalition won by a two-seat majority according to provisional results, is still awaited by individual courts of appeal within the coming days.
Prodi's new government is set to assume power in mid-May, after the new parliament, which convenes on April 28, elects a new state president.
The seven-year term of Carlo Azeglio Ciampi, the outgoing president, ends on May 18.
Prodi, a former European Commission president, faces an uphill task of putting together a durable government capable of sending a strong signal to the markets and kickstarting a stagnant economy, analysts said.
Economists said Prodi will likely appoint a leading financial expert as economy minister, rather than a career politician from within the coalition, a gesture designed to win immediate support from international markets.
Among the front-runners are Tommaso Padoa-Schioppa, a former board member of the European Central Bank, and Mario Monti, a former European competition commissioner.
In the short term, Prodi and his new government face a difficult time on the domestic front.
In addition to the administrative elections, there is the referendum in late June on legislation introduced by the Berlusconi government to grant greater devolved powers to Italy's regions.