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 LaLiga 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.
It took only six minutes for Levante to strike, Sergio Postigo's long ball completely missed by Raphael Varane, allowing captain Jose Luis Morales to round Thibaut Courtois and slide into an empty net.
Before they knew it, Madrid were two down. Varane handled when trying to challenge Marti, and after a lengthy VAR review led to a penalty award, the striker took the spot-kick himself and beat Courtois, who got a hand on it.
In a frantic period, Madrid thought they had one back when Marco Asensio headed in from under the bar after Casemiro's aerial effort smashed off the woodwork, but another long VAR review denied the hosts due to offside.
Madrid hit the bar again when Mariano Diaz sent a thumping header towards goal, while Lucas Vazquez somehow failed to beat Oier Olazabal from close range in another big opportunity.
Just before half-time, a magnificent Levante passing move, finished off by Ruben Rochina, was then ruled out through VAR due to offside in the build-up.
Lopetegui brought on Gareth Bale on at half-time, while Karim Benzema and Dani Ceballos soon followed.
But it took some time for the breakthrough, Marcelo lashing in a right-footed 15-yard strike after Benzema's assist.
The striker's curling 20-yard strike hit the post in the closing stages, and that was the nearest Madrid came to an equaliser, with Mariano's late tap-in ruled out for offside in a match that kept the officials busy.
Levante should have made it three at the death, Morales firing wide when clean through, before the final whistle was greeted by boos from the home fans.
What it means: Clasico or bust for Lopetegui… if he makes it that far
After making a bold team selection that included naming Bale, Toni Kroos and Benzema on the bench, another dreadful result here, coupled with an historically bad goalscoring streak, has him on the brink of the sack.
Olazabal does former club Barca a favour
Former Barcelona back-up Olazabal was going to have to play well if Levante were to record a famous win at the Santiago Bernabeu, and he certainly did.
Also helped by his woodwork which Madrid struck three times, Olazabal made 11 saves, his best being a close-range block with his leg on Vazquez just before the break. If it had gone in, all the momentum would have been with Madrid.
Varane at fault for Madrid
A four-time Champions League winner, Madrid have come to rely on Varane. But the decorated France international, fresh from winning the World Cup, has struggled this season and was particularly culpable in this game.
His mistake, failing to cut out a long ball from Postigo, allowed Morales to open the scoring and he then conceded the penalty for Levante's second. From there he was part of a Madrid defence that was wide open and regularly vulnerable to Levante's counter-attacks, the visitors having a third goal ruled out before the break.
Key Opta stats
3 - Marcelo has scored three goals against Levante in LaLiga, more than any other oponnent in the competition. Favourite. pic.twitter.com/YraZifDnig— OptaJose (@OptaJose) October 20, 2018
- Real Madrid hadn't conceded two goals in the opening 15 minutes in a single game in all competitions since February 2017 against Valencia
- They have only scored 12 goals in their opening nine LaLiga 2018-19 games, their worst scoring record since the 2004-05 season (8)
- Levante's Roger Marti has scored five goals in LaLiga this season, more than any other Spanish player in the competition (alongside Iago Aspas)
- Gareth Bale has failed to score in his last five LaLiga appearances; he had scored at least one goal in his previous seven games in the competition (eight goals in total)
- Julen Lopetegui is the first Madrid boss to lose three of his first nine LaLiga games in charge since Mariano Garcia Remon in 2004.
Madrid have to find a response at home to Plzen in the Champions League on Tuesday, but all eyes are already on their massive trip to Camp Nou to face rivals Barcelona in LaLiga on Sunday. Buoyed by a third straight league win, Levante host Leganes next Saturday.