Marica grabbed a deserved opener after 34 minutes when he rifled in following a spot of pinball in the box but he also deflected in substitute Fabio Quagliarella's header following a corner eight minutes from time.
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Juventus forward Quagliarella tried to claim the goal, having earlier come on for striker Balotelli who was subjected to racist booing from the crowd with the origins of the chants unclear.
However, Italian ultra fans did unveil a banner reading "no to a multi-ethnic national team".
"I am disappointed and angry, we give lots of speeches and then these things happen," Italy coach Cesare Prandelli told Rai television.
"But the lad must know that everyone has affection for him. I would like to see some sort of positive gesture towards him, maybe someone needs to give him a hug."
The Azzurri's last Euro 2012 qualifier at home to Serbia was abandoned after six minutes last month when right-wing away fans rioted but Italy have long struggled with their own "ultra" supporters with Romania having sporadic problems too.
Manchester City's Balotelli, Italy-born and of Ghanaian descent, was subjected to racist abuse from Juventus fans in particular while playing for Inter Milan as a teenager.
LEDESMA DEBUT
Prandelli handed debuts to four players, including Argentina-born midfielder Cristian Ledesma which has also upset the ultras, but the experimental line-up meant there was little fluency or cohesion.
Brescia's ex-West Ham United playmaker Alessandro Diamanti was anonymous and taken off at the break on his first appearance as a replacement for Antonio Cassano, dropped after being suspended by Sampdoria for swearing at the club president.
Balotelli returned in the rain and offered the only real first-half spark for Italy, managing two good shots, while substitute Alberto Gilardino was lively in the second period.
"We came up against a very aggressive side," Prandelli added. "In the second half we worked better, found more spaces. It was fantastic that we didn't want to lose this game."
Romania, struggling in fifth in Euro 2012 Group D in contrast to Italy who top Group C, looked composed on the ball except for being rattled by Gilardino after the break.
The only negative was defender Cristian Chivu limping off with a muscle injury after 15 minutes to hand faltering club side Inter Milan a fresh blow after a string of other injuries.
The friendly was played in Austrian Euro 2008 host city Klagenfurt for commercial reasons and because of its geographical position between Romania and Italy.
The Azzurri are back in qualifying action on March 25 in Slovenia while the Romanians visit Bosnia a day later.
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