The two sides appeared evenly matched in the opening stages, and it was a case of like against like as both sets of players displayed good technical skill and speed on and off the ball.
The closest either team came to scoring early on was after 11 minutes when Amajita midfielder Jino Moeketsi turned to face his own goal and sent an attempted back-pass just a metre wide of his own goal.
The host nation were to take the lead in the 23rd minute, courtesy of a well-worked move.
It started with a quick break that saw Snethemba Ngidi playing a brilliant through ball to Maselaelo Seango, who rounded keeper Matoshi Kushibiki.
Kushibiki, however, managed to get a slight touch on the ball, which saw it falling into the path of Thabani Mthembu, who had a relatively easy tap-in for his fifth goal of the tournament.
A minute later it could have been 2-0 when South Africa's pace again took them clear on goal, but after Asive Langwe's lob was parried by Kushibiki, Mthembu had his low drive cleared off the line.
Bidvest Wits midfielder Langwe was having his best game of the tournament and also came close to extending the scoreline when he curled a 30-yard shot just wide of the far post.
At times Amajita's interplay was breathtaking and in injury time they pieced together another brilliantly intricate yet fast flowing move, although Mthembu was too tightly marked to get in a decent effort on goal at the end of it.
After the restart Amajita kept up the pressure as Langwe continued to threaten the Japan goal, coming close in both the 46th and the 54th minutes.
Seango was also heavily involved in and around the Japan box, dragging an 18-yard shot inches wide before having a back post shot saved.
There was a rare chance for Japan after 50 minutes but Yuya Kubo's powerful drive was kept out by Gershi Kock.
Japan equalised against the run of play, scoring in the 70th minute when Masaya Matsumuto pulled the ball back for Shinya Yajima, who showed excellent control before scoring with a very well taken volley.
Closing action saw both sides having chances on goal, but Seango shot straight at Kushibiki while at the other end Kubo made space for himself before firing high into the stands.
The game then went straight to penalties and Amajita took the first advantage when substitute goalkeeper Lebo Ngubeni saved from Kubo.
But it was all even when Seun Ledwaba hit the post with his spot-kick.
Both sides then converted twice from the spot before Ngubeni made his second save, this time denying Matsumuto.
But Mthembu failed to put the game to bed as he also had his spot-kick saved.
More drama followed as Nguebi saved from Naoki Kawaguchi before Amajita captain Mbonegni Gumede finally secured the third place position for Solly Luvhengo's charges.