The South Korean side had three players sent off by Italian referee Roberto Rosetti including captain Hwang Jae-won and goalkeeper Shin Hwa-yong in what was far from a dirty match at Abu Dhabi's Mohammed bin Zayed stadium.
"The result doesn't reflect what we saw on the field and was made worse by the failures of the referee," Farias said.
"We could have achieved more in this competition, but football gives us situations that are very bitter and this today was the case."
Victorious Estudiantes coach Alejandro Sabella conceded his Argentine team were fortunate with some refereeing decisions, but said the Asian champions' dismissals were largely merited.
"Perhaps (Rosetti) whistled in favour of Estudiantes' superiority...but in general, he applied FIFA regulations to send off (the players) correctly.
"You will have different opinions, no-one is the owner of the truth.
"Three players is a lot for any team in the world, so obviously it was difficult for them."
Farias also said the seven-team tournament's structure favoured the European and South American champions, who receive a bye into the semi-finals, while his side beat DR Congo's TP Mazembe 2-1 at the quarter-final stage to set up their showdown with Estudiantes.
"Whoever came to the stadium could see the team that was rested," the Brazilian said.
"If they (Estudiantes) had started the competition maybe they wouldn't have got to the final.
"We could see clearly the (desire) to put Estudiantes in the (final) of the competition with Barcelona."
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