The songwriter took the stage for the final curtain call at Thursday's show wearing a purple jacket and metallic tracksuit pants and a matching tutu.
He remained there as the rest of the production's cast joined him to wave at the crowd and take their final bows.
While devotees were aware Elton was in the country, it seems even the cast and crew of the production were taken aback.
The official Instagram for Australia's Billy Elliot the Musical posted: "The company of Billy Elliot the Musical were surprised by a very special guest last night…SIR ELTON JOHN! Elton joined our cast on stage for the curtain call and the audience erupted into thunderous applause!"