Goals from Yosuke Ideguchi and Tetsushi Yamakawa in the 31st and 39th minutes respectively sealed a fourth win in five matches for the J-League champions, who moved clear of second-placed Melbourne City in the standings.
The first eight finishers in the 12-team eastern league phase progress to the last 16 in March, with the quarter-finals, semis and final due to be played in April in Saudi Arabia.
Shenhua had put the visitors under early pressure as Andre Luis hit the bar with a shot on the run in the 15th minute.
But Ideguchi gave Kobe the lead 16 minutes later when he was fed by Daiju Sasaki inside the penalty area and the midfielder bundled the ball past goalkeeper Bao Yaxiong.
The goal was initially ruled out for offside only for that decision to be overturned by a VAR review.
Eight minutes later the Japanese outfit doubled their advantage. Yuya Osako had been denied by Bao but from the resulting corner, Yamakawa flicked Nanasei Iino's centre beyond the keeper.
Shenhua were left to rue a series of missed opportunities, with Saulo Mineiro's effort midway through the second half ruled out for an infringement in the build-up.
Andre Luis then saw his penalty saved by Kobe's Shuichi Gonda eight minutes from time to cap a frustrating night for Leonid Slutsky's side.
Meanwhile, twice champions Ulsan HD of South Korea were held to a 0-0 draw by Thai visitors Buriram United.
That moved Ulsan into sixth place on eight points from five matches, while Buriram are eighth a further point behind.