However, Fernando Soriano leveled with a deflected shot in the 58th minute and Kalu Uche put lowly Almeria head just three minutes later as Real failed to clear a corner.
The Super Eagles should have broken the deadlock on 14 minutes when Kalu Uche set up Yakubu up to beat the offside trap but the Everton forward blasted wide with only Rachad Chitou at his mercy.
Over in Nigeria, Uche Kalu's first half brace and Junior Osagie's strike in the 75th minute helped Enyimba to a 3-0 victory over DR Congo's AS Vita Club in Aba to force the game into penalties.