The Russian driver flipped his car after skimming the grass beside the track on approach to the hairpin turn during his third qualifying run.
This weekend marks Formula One's first return to Suzuka since Jules Bianchi's ultimately fatal crash at the circuit last year
And while Kvyat thankfully walked away unhurt despite smashing into the barriers, his car appeared in far worse shape.
A wheel was missing as were large sections of the front nose and rear.
"It was a rookie mistake," Kvyat later said in comments carried by the official F1 website.
"I put two wheels on the grass and there was no run off area so it was a quite logical end I think."
"I'm sorry for the guys (in my team). It has been a tough couple of weeks already and with this crash it's extra work for the guys so I'm sorry about that."
The crash stopped the session ensuring no driver was able to complete their final qualifying run.
Rosberg had managed to record the fastest lap time of one minute 32.584 seconds at that point, just 0.076 seconds quicker than Mercedes teammate Lewis Hamilton who finished second fastest.
The Briton will be frustrated, however, at being denied another opportunity to beat Rosberg's time. A poor turn at the hairpin had cost him vital fractions earlier in the session.
Valtteri Bottas of Williams claimed third spot on the grid for Sunday's race while Ferrari's Sebastian Vettel secured fourth.
Mercedes back on track?
But for Mercedes, which has dominated F1 all season, Saturday was a return to form after a relatively poor showing in Singapore last weekend
Hamilton was forced to retire in the early in the iconic night-race while Rosberg could only finish fourth as Vettel sailed to victory.
"Great day today and a good comeback also for the team," Rosberg later told reporters in quotes carried by the official F1 website.
"It's fantastic after such a difficult weekend in Singapore to be back to back to our usual strength today," he added.
Driver's Championship leader Hamilton was gracious to his teammate conceding, "Nico is driving well this weekend."
He also appeared content with his car's performance in light of last week's retiral despite the abbreviated nature of the qualifying session.
"The car feels like normal, this weekend which is great to see," Hamilton said.
Best of the rest
Elsewhere on the track Saturday, Felipe Massa of Williams and Ferrari's Kimi Raikkonen claimed fifth and sixth positions respectively ahead of Kvyat's Red Bull teammate Daniel Ricciardo.
Kvyat will start Sunday's race in tenth position behind Romain Grosjean of Lotus and Force India's Sergio Perez due to his times in the Q1 and Q2 sessions.
Further down the grid there was further frustration for McLaren with Jenson Button failing to make it out of the Q1 session.
The 2009 champion will begin Sunday's race in 16th position, two places behind teammate Fernando Alonso who managed to scrape into Q2 to qualify 14th.