Inter, winners in 2006 when they beat three-times South American champions Sao Paulo in the final, lost 2-1 at the Morumbi in Brazil's biggest city but went through having won the first leg 1-0 in Porto Alegre last week.
They meet Guadalajara's in the two-leg final on August 11 and 18 after the Mexican side beat Universidad de Chile 3-1 on aggregate earlier in the week. Inter will host the second leg.
"We're satisfied to be in the Libertadores final, obviously very satisfied, but I feel a bit flat after this defeat. I think Internacional did not deserve to lose today," said coach Celso Roth, who took charge after Uruguayan Jorge Fossati was sacked despite having steered them into the semi-finals.
Inter had midfielder Tinga sent off 10 minutes from time for a second bookable offence but Sao Paulo failed to score a third goal despite enjoying the lion's share of possession.
Alex Silva headed Sao Paulo into a 1-0 half-time lead after a blunder by keeper Renan, who dropped an easy high ball.
Striker Alecsandro flicked in playmaker Andres d'Alessandro's free-kick in the 51st minute to equalise but Ricardo Oliveira restored the home side's lead less than two minutes later when he beat the offside trap and shot from the right.
Inter have already guaranteed a Club World Cup appearance in Abu Dhabi in December even if they were to lose the final since Mexican teams, from the CONCACAF region, are guests in the South American Confederation's (CSF) flagship event.
In 2006, Inter were crowned world club champions when they beat Barcelona, winners last year, in the final in Japan.
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