The 2013 semi-finalists safely assured their progression with a 3-2 victory over their Group E rivals after Lee's brace made him the competition's all-time leading scorer on 27.
Eduardo's opener and a Kosuke Taketomi brace put hosts Kashiwa well on top by half-time at the Kashiwa Hitachi Stadium.
Lee's brace, which included a stunning overhead kick, threatened a comeback and while it never materialised, the former Middlesbrough man etched his name into the history books nonetheless.
Shandong Luneng kept alive their hopes of qualifying alongside Kashiwa with a 3-1 victory over Vietnamese side Binh Duong.
Yang Xu and Junior Urso were on target in the victory at the Luneng Big Stadium.
Qualification from Group F remains up in the air after Gamba Osaka hammered 10-man Guangzhou R&F 5-0 - Patric and Hiroyuki Abe supplying a brace each.
It keeps Gamba in the mix for a place in the knockout stages with one game remaining, while R&F slip bottom.
"As the head coach I am responsible for the result, I am very disappointed and I have to apologise to the fans for letting them down," explained Cosmin Contra.
Leaders Seongnam saw off second-placed Buriram United 2-1 while Group A's bottom side Bunyodkor remain winless after Adrian Mierzejewski gave Al Nasr a 1-0 victory.
Persepolis and Lekhwiya also remain in the running for a qualification berth from the pool after the Qatari side completed a 3-0 victory over their group rivals in Doha.
Group B rivals Naft Tehran and Pakhtakor played out a 1-1 draw that keeps both their qualification hopes alive, with Vladimir Kozak cancelling out Gholamreza Rezaei's opener.
