Real won 4-2 on aggregate and Bale's cameo performance was one of few bright spots on a nervy evening for the hosts at the Santiago Bernabeu during which the Liga and European champions were in serious danger of being forced to play extra time.
Welsh international Bale brought badly needed quality to Zinedine Zidane's struggling side with a substitute appearance after 63 days out with injuries and had an instant impact.
With Real behind on the night after conceding an early goal, Bale picked up the ball after coming on to a smattering of applause and curled over a cross for Mayoral to head an equaliser in the 63rd minute which effectively ended the tie.
Bale also made Real's second goal, skipping into the area to force goalkeeper Pol Freixanet to parry and Mayoral picked up the loose ball to score again and put Real in front.
Fuenlabrada kept fighting, and substitute Alvaro Portilla salvaged a draw in the 89th, punishing some chaotic defending.
The visiting minnows from the suburbs of the Spanish capital had taken a surprise yet deserved lead through midfielder Luis Milla in the 25th minute with a stinging long-range shot which flummoxed home goalkeeper Keylor Navas.
Zidane again fielded a largely reserve team as he did in the 2-0 first-leg win but they were more than matched by Fuenlabrada, whose defender Cata Diaz had almost levelled the tie when his header hit the bar in the second half.
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