The 20-year-old superstar brought the tie level in the first half but after Danilo regained the hosts the advantage soon after the restart they shut up shop and held on to the win
The Musketeers held a 1-0 lead from the first leg but Neymar restored parity in the with his eighth goal of the tournament, joining Matias Alustiza as the tournament's top scorer, as he tapped in from close range. But the Timao managed to take control of the tie once more when Danilo slotted hom shortly after the break and they then shut out the Peixe in order to secure a famous victory in the Superclassico.
Muricy Ramalho lined up with three strikers for the match with last year's Brasileirao highest goal scorer Borges starting at the expense of Elano. Tite pulled no surprises with his line-up as Willian replaced the suspended Emerson Sheikh, but this left his side without a recognised striker.
Kick off was delayed after Santos' late entry to the pitch but as predicted they set out to attack from the off while Corinthians appeared happy to soak up the pressure. But the Timao looked dangerous on the counterattack and in the 11th minute a quick break, working the ball from right to left, ended with Willian producing a feeble shot from inside the area.
The Musketeers continued to play some crisp passing football in the Peixe half and 10 minutes later they won a free kick 25 yards from goal. Alex gave the visitors a scare as attempt to curl the ball into the top corner was turned behind off the fingertips of Rafael, knocking the post on its way.
Santos' attack was lacking tempo and focus which made it difficult for the visitors to penetrate the Corinthians defence and test Cassio. However, five minutes after Juan saw his deflected effort saved on the half-hour mark Tite's typically resilient defence was beaten.
Neymar broke forward at pace before slipping the ball to Alan Kardec on the right. He centred the ball from close to the byeline and Borges diverted it on goal. The striker's effort came back out off the post yet fortunately for the Peixe Neymar had followed in to tap in from close range.
Following the goal Corinthians' counterattacking became far more sporadic as they committed less men forward. After Ralf volleyed well over on the stroke of half time, Jorge Henrique saw his header from Fabio Santos' cross clawed away from goal in a brilliant save from Rafael.
With the game going to penalties as it stood due to there being no extra time or away goals, Liedson entered the fray as the hosts upped their search for a goal. And it only took them three second half minutes to find it as Alex's free kick from wide on the left was controlled by the unmarked Danilo at the back post who slotted a composed finish past the keeper.
The hosts soon returned to their defensive style and once more stifled the Santos forwards. Chances to test Cassio were again at a premium and a wayward effort from Juan midway through the second half was as good as it came for the reigning champions. For Corinthians, Alex's missile from a short free kick in the 75th minute was parried unorthodoxly away by Rafael.
Corinthians will now face the winner of the other semi-final between Universidad de Chile and Boca Juniors where the Argentines currently hold a 2-0 lead. The Timao will be looking to lift the trophy for the first time in their history.