After a goalless first half, John Owoeri came off the bench to score with his first touch of the ball in the 70th minute to put the Naze Millionaires ahead.
Inspite of Lobi's search for an equaliser, it was Heartland who scored again to extend their lead through Emeka Ogbu in the 89th minute.
Heartland are now the Super Four champions having finished top of the table with seven points from three games.
Kano Pillars defeated Rangers 2-0 to claim the second spot with six points, while Lobi Stars and Rangers Int'l finished in third and fourth place respectively with two and one point(s) each.
Heartland have now won two trophies this season, having defeated Kano Pillars 2-0 in the Super Cup played in Port Harcourt last December.