Parents form the body, Hashem gives the soul

בפסוק איש או"א תיראו ואת שבתותי תשמורו ודרשו חז"ל אם א"ל חלל את השבת אל תשמע לו.

On the pasuk, "Each person shall fear his mother and his father, and you shall keep My Shabbosos" — and Chazal expounded: if [a parent] tells you, "Desecrate the Shabbos," do not listen to him.

The Torah juxtaposes honoring parents with keeping Shabbos, and Chazal derive that obedience to parents stops where it would violate Shabbos. The Sefas Emes asks why Shabbos in particular is mentioned here.

ולמה פרט הכתוב מצות שבת בזה.

And why did the verse specify the mitzvah of Shabbos in this context?

He poses the question: of all mitzvos, why is Shabbos chosen as the limit of a parent's authority?

רק הרמז היא כי הקב"ה הקשה כיבוד או"א לכבודו ית"ש מפני שהם שותפין בו.

Rather, the hint is that the Holy One linked the honor of father and mother to His own honor, because they are partners in [the formation of] a person.

Chazal teach there are three partners in a person — father, mother, and Hashem — so honoring one's parents is bound up with honoring Hashem.

והגם כי כח אב ואם הכל מאתו ית"ש.

And even though the power of father and mother all comes from Him, may He be blessed.

Although ultimately the parents' creative power itself derives entirely from Hashem.

אבל יצירת הגוף בא באמצעיות אב ואם.

But the formation of the body comes through the agency of father and mother.

The physical body is produced through the parents as intermediaries — this is their share in the partnership.

אכן הנשמה היא כח אלקי בלי השתתפות.

However, the neshamah is a Divine power, without any partnership.

The soul, by contrast, comes directly from Hashem alone — no parent has any share in it.

וזה עצמו ענין השבת במעשה בראשית שנברא הבריאה בדרך הטבע וזה ששת ימי המעשה.

And this very thing is the matter of Shabbos in the work of creation, for the creation was made by way of nature, and this is the six days of activity.

The same pattern appears in creation: the six weekdays produced the natural, physical world.

ואח"כ בשבת ניתן כח אלקות בחי' הנשמה של העולם כמ"ש וינפש.

And afterward, on Shabbos, the power of Godliness was given — the aspect of the "soul" of the world — as it says, "and He rested (vayinafash)."

Shabbos added a Divine dimension, a "soul," to the otherwise natural world — alluded to in "vayinafash," related to nefesh (soul).

וזה קיום כל מעשה בראשית.

And this is the sustaining force of all of creation.

This indwelling Divine "soul" given on Shabbos is what keeps all of creation in existence.

וכמו כן באדם הכנת הגוף באמצעיות אב ואם כעין בחי' ימי המעשה ואח"כ שורה עליו הנשמה בחי' השבת יומא דנשמתין ולאו דגופא.

And likewise in a person: the preparation of the body is through the agency of father and mother, akin to the aspect of the weekdays, and afterward the neshamah rests upon him — the aspect of Shabbos, "the day of souls and not of the body."

The same two-stage pattern operates in man: the parents form the body (like the weekdays), and then Hashem alone places the soul within (like Shabbos, the day belonging to the soul, not the body).

וצריך האדם להיות זהיר ביותר בחלק הנשמה.

And a person must be especially careful regarding the portion of the neshamah.

Since the soul is purely Divine, a person must guard it with particular care.

זהו ואת שבתותי תשמורו:

This is the meaning of "and you shall keep My Shabbosos."

Guarding Shabbos — the "soul" dimension that belongs to Hashem alone — is therefore set as the limit beyond which even parental honor does not extend, for the soul is wholly Hashem's.

Summary: The Torah pairs honoring parents with keeping Shabbos because, just as parents and Hashem are the three partners in a person, the body is formed through the parents (like the six weekdays of natural creation), while the soul is purely Divine, with no partner (like Shabbos, when Hashem placed a "soul" into the world). Since Shabbos corresponds to that exclusively Divine portion — the soul that belongs to Hashem alone — it marks the boundary of parental authority: one must guard "My Shabbosos" even against a parent's command, taking special care of the soul-dimension that is wholly Hashem's.