The piece you remember is

SEGUNDA GÉNESIS
(“Second Genesis”), written by Carlos Trillo and drawn by Horacio Altuna.

What it is
• A one-off short story (14 pages) that the two Argentine masters produced in the mid-1970s for the weekly magazine Skorpio.
• It was reprinted many times afterwards, both in Argentina and in Spain, in the big anthology magazines 1984, Zona 84 and Cimoc; that is almost certainly the thick Spanish-language magazine you borrowed in the early 1990s.
• Heavy Metal (U.S.A.), vol. 6 № 9, December 1982, ran the first English version, also titled “Second Genesis”.

Story outline (matches the memories you listed)

1. Nazi-occupied Eastern Europe, 1944. Gestapo men burst into the flat of Professor Levin, a Jewish scientist who has secretly built a time machine.
2. With Levin are two Jewish children, a boy and a girl who are not related (their names are never given at this point).
3. In the mêlée the device is activated prematurely. It pulls in a nearby Luftwaffe pilot (with his Messerschmitt, which immediately crashes) and hurls all four of them far into Earth’s prehistory.
4. The wreck lies in a warm, luxuriant jungle devoid of other human beings.
5. The professor spends years trying to repair the burnt-out circuitry while the unlikely quartet learns to survive. The German, who proves to be decent rather than fanatical, distils cider from wild apples and keeps himself half-drunk most of the time.
6. When the machine is finally patched up the children have grown into a strapping youth clad in a loin-cloth and a statuesque girl in a fur bikini. The pilot decides that, before civilisation can begin anew, the youngsters ought to know “how things are done” and gives them a discreet lesson in sex.
7. The professor catches him spying on the results, furiously drags him into the machine and makes a “test jump”. The device vanishes and is never seen again.
8. Alone, the girl says, “¿Qué haremos ahora, Adán?” – and only here do we learn his name. “Nos las arreglaremos, Evie”, he answers.
9. A final caption explains that the drunken pilot, tempting them with fermented apple juice and “knowledge”, will go down in legend as “the Serpent”, and that this is the true origin of the Garden of Eden story.

Why all the details fit

• Period, place and Jewish children under the Gestapo – exactly as in the comic.
• A single German airman is swept along; his whole plane crashes in the jungle.
• Many years elapse, the children reach puberty in skins, the pilot provides the “forbidden-fruit” lesson, and the professor disappears with him in a last time-jump.
• The punch-line with the kids suddenly called Adam and Evie, and the closing narration equating the tipsy pilot with the biblical Serpent, is reproduced almost verbatim from Trillo’s script.

Where to find it now

• Spanish collections: “Trillo & Altuna – Historias fantásticas” (Toutain Editor), “Altuna – Fábulas” (Planeta/DeAgostini) or the volume “Horacio Altuna – Obras completas 1”.
• English: Heavy Metal magazine, December 1982 issue, or the trade paperback “Time-Travel Tales” (Catalan Communications, 1987).
• French: Métal Hurlant n° 87 (“Seconde Genèse”).
• Italian: L’Eternauta n° 15 (“Seconda Genesi”).

So the WWII time-machine comic that turns its young Jewish protagonists into the legendary Adam and Eve is Carlos Trillo & Horacio Altuna’s SEGUNDA GÉNESIS / SECOND GENESIS.