Defence dominated the early stages and it was two minutes into the game before Clinton scored the first basket of the encounter.
Callum Mcrae scored the next basket for the Kiwis and the big Kiwi centre was also prominent at the defensive end with three rebounds and a block in the quarter.
A tight first period ended with New Zealand 12-8 ahead.
A Sam Waardenburg put back got the scoreboard moving in the second stanza and a Taki Fahrensohn three took New Zealand to a 17-10 lead forcing a concerned Australian coach to call a timeout.
Hamish McDonald connected with a triple followed by a jump shot as New Zealand moved to a 24-16 lead. An excellent first half defensive effort from the JTB's finished with them ahead 27-20. Waardenburg led all scorers and rebounders at the interval with seven points and six boards.
A pair of Clinton triples took the JTB's to a double digit advantage but Australia responded with a 10-0 run. That run was broken by Taane Samuel but a strong Australian third period ended with the JTB's just three points ahead, 40-37.
Flynn Cameron scored with a left handed drive but another Australia run took Australia into the lead 44-42 with seven minutes to play.
Waardenburg tied the scores only for Australia to reclaim the advantage. The Kiwis offence had gone cold but a turn-around jumper by Samuel moved the JTB's within two points, 48-46, with three to play.
After that it became the Clinton and Samuel show as the Junior Tall Blacks created history.
Basketball New Zealand Chief Executive Iain Potter described the victory as, "A great achievement by the team and the coaching staff and an historic moment for New Zealand basketball. The win once again highlights the enormous amount of talent that we have emerging from our national and local development programmes."
Junior Tall Blacks 57 (Clinton 14, Samuel 11, Waardenburg 11 + 12 rebounds)
Australia 51