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."
Benitez put Estudiantes ahead in first-half stoppage time when he slipped the offside trap to get behind Hwang at a free kick and steered the ball gently with his head inside the near post.
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.
Estudiantes almost scored an early goal in the sixth minute when Shin failed to hold a long range shot from Rodrigo Brana and the lurking Mauro Boselli hit the post with an overhead kick. Benitez then blasted the rebound over.
The Argentine side gradually slid back into their more natural counter-attacking style as the Steelers became more daring and had a couple of shots on target that Albil held comfortably.
Pohang right-back Choi Hyo-jin spoilt a good chance for an equaliser in a fast counter-attack down the right, attempting a shot from a tight angle that went over when it would have been better to pulll the ball back into the middle.
Estudiantes right back Clemente Rodriguez could have scored a third goal for Estudiantes in the dying minutes but his shot came off the post.
