Shea was also the first player to score at TQL Stadium in Miami's 3-2 win at Cincinnati back on May 16, the first MLS match played at the stadium.
His late match-winner gives Miami (7-9-5, 26 points) its fifth victory in eight matches and second in two games in Cincy.
The Flamengos now sit 10th in the Eastern Conference, just four points behind seventh-place D.C. for the East's final playoff spot.
Meanwhile, Cincinnati (3-10-8, 17 points) is nine games into life at their new home without a win, having lost here after five consecutive home draws to remain 13th in the East, ahead of only Toronto.
The hosts might have had slightly more chances before Miami's winner, but not many, putting only two of their 10 shots on target.
Miami hadn't put any of their previous nine shots on frame prior to Shea's winner, but he made no mistake after Nicolas Figal found him with a simple diagonal ball from the back.
Cincinnati had five defenders back, but Shea had snuck behind the right wingback and stayed onside via center back Geoff Cameron to run onto the ball.
Shea had arguably Miami's best chance prior to that, when he had an open look from inside the left side of the penalty before halftime area that he slammed into a teammate with the goal gaping.
Cincy started pressuring more after the break, with Brenner coming the closest to scoring.
In the 58th minute, he headed a corner kick just wide of the left post. In the 75th, he appeared to have an open look at goal, but was closed down after failing to take a shot early.