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Second-half substitute Merino converted from close range after goalkeeper Bart Verbruggen had parried Nico Williams' low shot into his path.
Williams had earlier given Luis de la Fuente's European champions a first-half lead with a smart finish.
The Netherlands responded well and equalised before the hour mark when Cody Gakpo powered home a low shot from Justin Kluivert's pass.
Tijjani Reijnders low shot 39 seconds into the second period appeared to have earned the visitors a narrow lead to take into the second leg, but after Hato was dismissed with seven minutes remaining, Merino struck to salvage a draw for the holders.
Merino's late goal stretches Spain's unbeaten run in all competitions to 17 matches - since a 1-0 friendly defeat by Colombia in March last year.
The second leg takes place in Valencia on Sunday, with the winners of the tie facing either Croatia or France in the semi-finals.
