Rebic swept home Samu Castillejo's low pull back in he 25th minute to consign to draw Milan level on 35 points with Hellas Verona, who currently occupy the final Europa League spot on goal difference.
Rebic's winning goal was his sixth in seven games in all competitions, a run that comes after failing to score at all in the first half of the season.
The Croatian's strike helped the hosts bounce back from last week's derby disappointment against Inter Milan to continue a positive run under coach Stefano Pioli that also saw them unlucky not to beat Juventus in the Coppa Italia semi-final first leg last week.
They have lost just once since the turn of the year - to title-chasing Inter - and are playing well enough to aim for European football next season.