The Brazilian forward beat the offside trap to nod home the only goal on an evening to forget for Federico Piovaccari, who had an effort of his own disallowed in the first half and was sent off late on for elbowing Edu Albacar.
The home side thought they had broken the deadlock on the stroke of half-time when Piovaccari's header had goalkeeper Przemyslaw Tyton scrambling across his goalline in an attempt to keep it out.
But any celebrations were cut short through a combination of confusion over whether the ball had crossed the line and by an offside flag.
And Elche made the most of the reprieve by edging ahead five minutes after the restart.
Albacar's in-swinging free-kick floated as far as Jonathas and his flicked header deceived Xabi Irureta, who led protests for offside that fell on deaf ears.
Eibar were reduced to 10 men with 12 minutes remaining when Piovaccari was given a straight red card for catching Albacar in the face with a forearm as the duo tussled for an aerial ball.
Victory gives Elche a four-point cushion over third-bottom Granada.
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