Qui-Gon did originally disappear, but the scene was cut down in editing.
EXT. THEED - CENTRAL PLAZA - FUNERAL TEMPLE STEPS - SUNSET
QUI-GON's body goes up in flames as the JEDI COUNCIL, the
QUEEN, SIO BIBBLE, Capt. Panaka, the HANDMAIDENS, and ABOUT
ONE HUNDRED NABOO TROOPES, TWENTY OTHER JEDI, PALPATINE, OBI-
WAN (standing with ANAKIN), JAR JAR, BOSS NASS, and TWENTY
OTHER GUNGAN WARRIORS watch. There is a drum roll that stops.
Doves are released, and the body is gone. ANAKIN looks to
He is one with the Force, Anakin...You
must let go.
What will happen to me now?
I am your Master now. You will become
a Jedi, I promise.
Wow. It would have been so much better if that scene was left intact. All Lucas had to do was cut five seconds of Jar Jar screen time to make room for it.