The Madrid boss made five changes on Saturday in a bid to end a run of four games without a win or a goal.
But Jose Luis Morales and a Roger Marti penalty put Levante two up inside 13 minutes in a dramatic match that included three VAR reviews.
Madrid broke their club record for the longest goalless run in their 116-year history by failing to score in the first 56 minutes, a streak finally ended by Marcelo's strike 18 minutes from time.
But despite hitting the woodwork on three occasions, Madrid fell to defeat that leaves Lopetegui under further pressure to save his job, with the Clasico taking place in just eight days' time.
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