* PM wins vote of confidence in second attempt
* Forms minority government with Social Democrats
* Backing of Communist to give it majority, draws protest
* Babis was clear election winner, struggled to get majority (Adds vote result, protest)
By Petra Vodstrcilova and Jan Lopatka
PRAGUE, July 12 (Reuters) - The Czech parliament gave its backing early on Thursday to a new, centre-left minority cabinet led by billionaire Andrej Babis, ending his nearly nine-month effort to secure a parliamentary majority.
The new government, which pairs Babis's ANO party with the Social Democrats, relied on the support on the Communist Party, giving it a political say for the first time since the fall of communism in the former Czechoslovakia in 1989.
Most parties have rejected working with Babis, whose ANO won an election last October, because he faces fraud charges related to a 2 million euro ($2.34 million) European Union subsidy a decade ago. He has denied any wrongdoing.
Under a deal that has been criticised by opposition parties, ANO and the centre-left Social Democrats together hold 93 seats in the 200-seat lower house of parliament, with the pro-Moscow, anti-NATO Communists agreeing to lend another 15 votes.
After 16 hours of debate, the government won 105 votes among the 196 present in the ballot, which is mandatory for any new cabinet, official results showed.
"I want to ... stress that this is a very serious moment, the return of the Communist Party to power and influence in the Czech Republic," Petr Fiala, leader of the main opposition party, centre-right Civic Democrats, said in parliament.
Speaking before the debate, Babis said his government would focus on investment and maintaining sound public finances, which have been in surplus in recent years amid a period of strong growth as well as a labour market with the EU's lowest unemployment.
He also aimed to give the country a stronger voice in the EU and continue to push the bloc to strengthen security to get immigration under control.
"We will continue to be active, and make effective alliances" in this, Babis said.
Babis' appeal stems from his image as someone who can dislodge the country's mainstream parties, seen by many voters as riddled with corruption. His rise to the top of Czech politics has mirrored the progress made by populist movements across a number of EU countries.
Opponents, however, accuse him of eroding democracy due to the vast empire he built in chemicals, farming and the media. He has transferred control of the group to a trust fund to comply with conflict of interest laws.
Hundreds of protesters chanted slogans against Babis outside parliament for hours as the house debated the confidence motion. At one point, Babis walked out to meet the crowd, but returned inside soon after protesters threw at least one bottle of water at him, news agency CTK reported.
Babis has repeatedly said he would keep the Czech Republic on a pro-Western course and avoid the kind of sparring over checks and balances that has landed neighbouring Poland and Hungary in conflict with Brussels.
But he backs Central European peers in rejecting to accept asylum seekers fleeing war in the Middle East and Northern Africa. His hard line reflects public mood in a country where six in 10 refuse to accept any war refugees, according to surveys, and nearly all those remaining say they would only provide temporary asylum.
The Communist Party leadership agreed to back the new administration even though Babis, who has been caretaker prime minister since a first attempt to win confidence for a one-party cabinet failed in January, refused some of their demands.
One was for cutbacks in the Czech contribution to NATO military missions abroad. Another sought representation on the supervisory board of the biggest state-controlled company, electricity producer CEZ.
Babis did agree with the Communists on issues like taxing property returned to churches after earlier communist confiscations, and on and raising pensions.
The Communists are allied with pro-Russian President Milos Zeman, and their role in supporting the cabinet will give the president more political leverage. ($1 = 0.8565 euro) (Reporting by Petra Vodstrcilova and Jan Lopatka; additional reporting by Jason Hovet; editing by Catherine Evans and G Crosse)
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