The Brazilian side won the semi-final tie 4-3 on aggregate having beaten Cerro 1-0 at home in last week's first leg.
However, captain Edu Dracena will miss the final after being sent off in added-time.
Santos, champions in 1962 and 1963 during Pele's heyday, face either Velez Sarsfield of Argentina or Penarol of Uruguay, who meet in the second leg of their tie in Buenos Aires on Thursday. Penarol won the first leg 1-0.
"They played the better football, we put in the fighting spirit. They are a very good side and they have Neymar, who makes the difference," Cerro's Juan Manuel Lucero told Fox Sports.
Santos, improving with each match since coach Muricy Ramalho took charge eight weeks ago, went ahead in the third minute.
Brazil midfielder Elano hit a right-footed free kick from the left, following a foul on Neymar, to the near post where Ze Eduardo's glancing header beat goalkeeper Diego Barreto.
BIZARRE OWN-GOAL
Close to the half hour, Barreto's bizarre mistake handed Santos their second via an own goal by the Paraguay keeper.
Neymar ran for a high ball out of defence from Edu Dracena, scorer of the only goal in the first leg, deep into Cerro territory with two defenders chasing.
As the trio entered the box, centre back Pedro Benitez rose above Neymar to head the ball towards the advancing Barreto who seemed to be surprised by the flight of the ball and his attempted punch merely helped it over his head into the net.
Cerro, who have never reached the final, reacted quickly and pulled a goal back less than four minutes later, left back Cesar Benitez heading home Argentine youth international Juan Iturbe's curling corner.
However, Neymar added a third for the visitors in first-half injury time when he took a pass from midfielder Arouca, stepped inside a defender and deceived Barreto with a low shot inside the near post.
Battling Cerro pulled another goal back after an hour when striker Fredy Bareiro headed down a cross from the right and substitute midfielder Lucero volleyed past Rafael.
The home side pinned Santos back in the final quarter of an hour and midfielder Jonathan Fabbro struck a superb equaliser from 25 metres into the top corner nine minutes from time.
Cerro, who hit the bar in added-time, salvaged some pride after a disappointing start but were left still needing two goals to win the tie with Santos holding the insurance of their away goals.
Santos last reached the final in 2003 when they lost to Boca Juniors of Argentina.
