The Saitama-based side are this season's surprise packages and continue to defy the odds although their cause was helped today by Kofu striker Masaru Matsuhashi's dismissal in the second minute, with Novakovic putting the visitors on the front foot from the penalty spot shortly afterwards.
Kosuke Kikuchi doubled their lead in the 20th minute before Novakovic added a third just before half-time.
Yokohama F. Marinos ensured they did not slip further behind the league leaders after they edged out Sagan Tosu 1-0.
It seemed the second-placed side would be forced to settle for a goalless draw - which would have seen them slip seven points off the pace - but Seitaro Tomisawa popped up in the 77th minute to seal the spoils for Yokohama.
Kashima Antlers remain in third after coming from two goals down to see off FC Tokyo 3-2.
The capital club took a surprise seventh-minute lead through Tadanari Lee before Kazuma Watanabe stunned the home crowd even further just before the interval.
However, Yuya Osako superbly led the fightback with strikes in the 47th and 65th minute in between Hyun-Soo Jang's own goal just before the hour mark to complete a remarkable turnaround.
Defending champions Sanfrecce Hiroshima remain nine points adrift of Omiya Ardija despite a 2-0 win at Shonan Bellmare.
Yojiro Takahagi put Sanfrecce ahead in the 18th minute before Mihael Mikic ultimately sealed victory on the stroke of half-time.
Hiroki Yamada's 80th-minute strike denied rock-bottom Oita Trinita a crucial three points at home to fellow strugglers Jubilo Iwata.
Both sides had collected just six points from their opening 12 games before today although the hosts looked on course for just their second win of the season when Daiki Takamatsu broke the deadlock in the 62nd minute before Yamada levelled proceedings late on.
Cerezo Osaka claimed a 2-1 win against Nagoya Grampus Eight, who failed to capitalise after scoring a late goal.
The hosts were firmly on the way to the points when Cunha Edno and Yoichiro Kakitani scored in the 57th and 67th minutes respectively and while Joshua Kennedy halved the deficit in the final minute, it proved too little, too late.
Yosuke Kawai and substitute Toshiyuki Takagi bagged second-half goals to give Shimizu S-Pulse a 2-0 win over Vegalta Sendai, while Yoshito Okubo's brace helped Kawasaki Frontale edge to a 2-1 win over Albirex Niigata, who had levelled through Musashi Suzuki.