A crowd of more than 17,000 spectators erupted in celebration as the 38-year-old headed home in the 78th minute on Sunday to reach the landmark against Jeju United in the southwestern city of Jeonju.
Lee rushed towards the stands, taking off his green jersey and waving it at the roaring home fans.
"I always compete thinking that this could be my last match," Lee told reporters after Sunday's victory.
"I have the thought that I might not be on the ground next year," he added, hinting at a possible plan to retire.
Lee made his K-League debut in 1998 with Pohang Steelers before he joining Jeonbuk in 2009, with whom he has scored 136 goals.