The Argentine is unhappy after the Nerazzurri were denied a spot-kick following a tackle on Esteban Cambiasso on Saturday
Esteban Cambiasso went to ground in the penalty area in the second half on Saturday afternoon, in their 2-1 defeat at San Siro, but referee Nicola Rizzoli dismissed the protests of the home side.
Zanetti slammed the official behind Gianluigi Buffon's goalmouth but praised his side for showing heart in pushing Antonio Conte's men all the way until the final whistle.
"There were things that we saw differently but he decided otherwise," the Argentine told the club's official news channel after the game. "It looked like a clear penalty on Cassano in the second half. "The goal-line ref was put there to help out in situations like this. If he doesn't do that then there's not much point.
"It was a good performance in the end. We're disappointed to lose because they scored their second when we were having our best spell.
"We threw the kitchen sink at them trying to find an equaliser but we just couldn't get it despite creating some great chances. It's a shame but at least we can take heart from the performance that we produced against a great team like Juventus."
Goals from Fabio Quagliarella and Alessandro Matri secured an away win for the Bianconeri, despite Rodrigo Palacio's equaliser just after half-time.
But the main talking point after the match was Cambiasso's red card for an awful challenge on Sebastian Giovinco in stoppage time - a tackle which Zanetti was quick to condemn.
"It was just a nasty foul, he made a late challenge," the Argentine said of his compatriot. "It's the first time he's been sent off in his career, though.
"I heard that somebody on TV said he deserves a five-match ban. Let's not blow it out of proportion, come on."
The Nerazzurri's latest defeat saw them drop to seventh in Serie A, and though their Champions League qualification hopes are dwindling, Zanetti is confident that if they win crucial clashes in the next two months a top three spot is still possible.
"We need to find the strength to do as best as possible in the remaining games, find the strength to put in a good performance in Genoa like we did today against a top team like Juventus," the Inter skipper continued.
"Third place [is possible] as we still have a few six-pointers to play and a game in hand. Let's see what happens between now and the end of the season."