Second-stage runnerup Gamba Osaka became the latest side to suffer an Emperor's Cup upset as it went down 1-0 to second-division Kawasaki Frontale in the fourth round on Sunday.
Jubilo Iwata, which sealed the first-ever J. League double earlier this month, beat second-division champion Oita Trinita 2-0 to move into the last eight but Nabisco Cup winner Kashima Antlers and holder Shimizu S-Pulse both needed extra time to edge past J2 opponents.
Five top-flight teams crashed out when the first-division sides entered the tournament in last week's third round including Vissel Kobe after losing to Kawasaki.
Frontale claimed its second first-division scalp in a week when Yasutaka Kobayashi found himself totally unmarked in the 83rd minute to claim the only goal of the game against Gamba.
The transfer of Japan star Naohiro Takahara to German side Hamburg SV dominated the build-up to Jubilo's game against Oita but it was veteran strike partner Masashi Nakayama who opened the scoring after 37 minutes, pouncing on a dreadful error by Oita keeper Hayato Okanaka.
Substitute Ryoichi Maeda, who came on for a disappointing Takahara midway through the second half, sealed the win with a header from a corner 15 minutes from time.
Elsewhere, South Korean striker Ahn Jung Hwan headed home the winner in the last minute of extra time as Shimizu struggled past Shonan Bellmare 3-2 while Brazilian forward Euller scored 13 minutes into extra time as Kashima edged out Omiya Ardija 1-0.
Relegated Sanfrecce Hiroshima came from behind to beat Yokohama F Marinos 2-1 while Nagoya Grampus Eight thrashed Cerezo Osaka 5-2. Kyoto Purple Sanga downed Avispa Fukuoka 1-0 after extra time and JEF United Ichihara defeated Vegalta Sendai 2-1.
The quarterfinals take place Wednesday.