The 34-year-old had been waiting three months to hit the milestone figure and, having finally found it with an impressive volley, Simeone was full of praise for the soon-to-depart striker.
"Fernando is an icon here, whether he's scoring goals or not," he told reporters at his post-match press conference. "He's earned this status and respect through hard work.
"When I called him to sign for us, I told him I wanted him to come as a football player and not an idol. Fernando's performance was as important as that of the whole team.
"We made three very beautiful goals, and having everybody pulling in the same direction is what works for the team. People care that Fernando has incredible feelings for this club, it makes me happy to have helped him live with this team once again."
Atletico remain second in the La Liga standings, four points in front of Real Madrid.