Chilton conjured arguably one of his best qualifying laps this year to leave not only Bianchi trailing, but also Caterham duo Charles Pic and Giedo van der Garde.
The only other occasion Chilton managed to get the better of Bianchi on a Saturday was around Monaco, but then only because the Frenchman suffered an engine issue and failed to set a timed lap.
On this occasion, ahead of the Japanese Grand Prix and on one of the most difficult tracks to master in Suzuka, the 22-year-old from Reigate finished six tenths of a second ahead of Bianchi.
It could be argued Bianchi was carrying an elbow injury following his crash in first practice on Friday that resulted in him missing the second session due to the damage to his car, but Chilton refused to let that belittle his achievement.
"We all know this circuit is pretty challenging, not an easy one to learn, so I'm really, really happy with the outcome," said Chilton, speaking to Press Association Sport.
"To have out-qualified both Caterhams, and they look like they've a bit more pace than us this weekend, to get a lap in I was happy with, and with the team playing its cards right, it paid off.
"This is definitely the monkey off my back."
Chilton has been edging ever closer to Bianchi in recent qualifying sessions, finishing two tenths of a second down in Belgium, a tenth off in Singapore, and 0.151secs adrift last time out in Korea.
"Since the August break it has been really, really close, nothing between us," added Chilton.
"In Monza, if fuel corrected, I'd have done it. In Singapore there was only a tenth between us over a two-minute lap.
"It's nice to have an even fight, and at a challenging track neither of us knew coming here, so I'm really happy."