Santos forward Neymar was a threat from the start as he hit the post in the opening five minutes before giving the South American champions the lead in the 19th by curling a left-footed shot into the upper corner of the net.
Borges doubled the lead for Santos five minutes later when he scored from the edge of the penalty area, but Kashiwa's Hiroki Sakai pulled a goal back for his team nine minutes into the second half with a header.
However, Santos proved too strong and Danilo restored the two-goal lead with a well-taken free kick in the 63rd minute before Ibson rattled the crossbar for the Brazilian side.
Barcelona will face Qatar���s Al Sadd in the other semifinal on Thursday, with the winner facing Santos in Sunday's final.
The match for fifth place on Wednesday saw Mexican side Monterrey claim a 3-2 victory over Esperance.
Monterrey fell behind by a goal to Yannick Ndjeng just after the half-hour mark, but responded with goals from Hiram Mier, Aldo De Nigris and Jesus Zavala before a penalty kick from Khaled Mouelhi reduced the deficit to one goal 15 minutes from time.