After a cagey first half, the Rabat based side took control following the break. Ahmed Hammoudan opened the scoring in the 58th minute, reacting quickest to finish from close range after a rebound.
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The hosts maintained their pressure and doubled their lead in the 79th minute, with substitute Khalid Ait Ourkhan firing home after a defensive lapse.
The result gives FAR Rabat a strong advantage heading into the return leg in Berkane on April 18.
Berkane now face an uphill battle to overturn the deficit, while FAR Rabat will be confident of sealing their place in the final with another disciplined performance.