Steelers had three players sent-off, including captain Hwang Jae-won and goalkeeper Shin Hwa-yong, in the second half, with goalscorer Denilson taking over in goal.
"We could have achieved more in this competition, but football gives us situations that are very bitter and this today was the case," Pohang's Brazilian coach Sergio Farias told a news conference.
"The result doesn't reflect what we saw on the field and was made worse by the failures by the referee. I'm not talking about a conspiracy, but the failures of the referee," he added, referring to Italian Roberto Rosetti.
Estudiantes coach Alejandro Sabella said: "Perhaps (Rosetti) whistled in favour of Estudiantes' superiority...but in general, he applied FIFA regulations to send off (the players) correctly."
He increased Estudiantes' lead eight minutes into the second half before Brazilian striker Denilson pulled one back in the 71st when the Korean side were already down to 10 men, Hwang having been sent off for a second booking after a body check on wing Maxi Nunez.
Midfielder Kim Jae-sung was sent off in the 72nd minute for a foul on Juan Sebastian Veron, his second yellow, and keeper Shin got a straight red 12 minutes from time for a foul on Nunez outside his box as both raced for a long ball out of the Estudiantes half.
DENILSON STRIKE
In Saturday's final, South American champions Estudiantes will meet the winners of Wednesday's semi-final between title favourites Barcelona and Atlante of Mexico.
Benitez scored his second goal when Enzo Perez lobbed over the keeper and Benitez's shot from the left, which Kim Jae-sung failed to block, went in off the far post.
Denilson, scorer of both goals in Pohang's 2-1 win over TP Mazembe of DR Congo in their quarter-final, scored in the 71st minute when he latched onto a poor clearance in the Estudiantes box to beat goalkeeper Damian Albil from close range.
