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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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.
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.
"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."
