The reigning Australian champions went into the game in Gosford two points behind Western Sydney with three games left of the regular season.
And Ibini-Isei's late goal earned Central Coast a 2-1 win that puts them in pole position to finish second behind runaway leaders Brisbane Roar ahead of the Final Series.
Joshua Rose put Phil Moss' side ahead just after the half-hour mark, only for Nikolai Topor-Stanley to level matters five minutes before the break.
The game looked set to end all square, but Ibini-Isei had other ideas, popping up with his fifth A-League goal of the season to seal a valuable three points for the hosts.
In Saturday's other match, Melbourne Victory missed the chance to overtake Western Sydney as they were held to a 1-1 home draw by Sydney FC.
Sydney forward Joel Chianese broke the deadlock for the visitors shortly after half-time, but James Troisi spared Victory's blushes by snatching an equaliser in the 64th minute.
The draw leaves the Victory fourth, while Sydney are sixth.
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