According to Rambam and the Sefer HaChinuch (and other mitzva counters, but not all), we go back to Parshat B'shalach for the first of the Torah's five mitzvot concerning Shabbat.
Specifically, we find there, in the context of the episode of the MAHN (manna), the command not to leave one's place on Shabbat. In the context of the story, this command was given to the Exodus generation, referring to their not going out of the camp to collect MAHN, as none would fall on Shabbat and that which was prepared from Friday's double amount would provide food for the people on Shabbat.
That alone would not make a mitzva among the 613 (TARYAG), because it is not a prohibition that would continue throughout the generations. But there is an aspect of that command that is for all times – T'CHUM SHABBAT, the Shabbat boundary.
Without too much detail, this is the prohibition of walking more than a certain distance outside your place of dwelling – be it a big city or an individual home out in the boondocks. Then we move to the next sedra, Yitro, for the two mitzvot that are found in Commandment #4 of the Aseret HaDibrot.
First, the positive command of ZACHOR, which is fulfilled – first and foremost – by Kiddush on Friday night, i.e. as Shabbat enters – both in davening and at the dinner table. Havdala is part of ZACHOR ET YOM HASHABBAT L'KAD'SHO too, as Shabbat exits. Many other things we do on Shabbat and throughout the week, are also related to the fulfillment of the spirit of this mitzva. An example, referring to the days of the week by there numbers to Shabbat rather than by the names we have come to use, is a fulfillment of ZACHOR.
This is followed by the "major" prohibition of Shabbat – that of doing any manner of MELACHA, the forbidden creative activities on Shabbat. These include 39 different categories of Melacha and countless TOLADOT, derivatives or offshoots, which are on the same level of prohibition as the AVOT MELACHA. Cooking, for example, is a TOLADA of Baking; watering the grass is a TOLADA of planting.
This brings us to Parshat Mishpatim where we find a positive command which is the other side of the MELACHA-prohibiting mitzva. "And on the seventh day you shall rest." This does not refer to a Shabbat afternoon nap. That's part of the Rabbinic concept – inspired by the Navi – of Oneg Shabbat. The positive Torah mitzva to rest means to abstain from Melacha.
Everything that is a violation of the prohibition of Melacha is also a violation (non-fulfillment) of TISHBOT (you shall rest). No mention of Shabbat in T'ruma or T'tzaveh – just Mikdash (Mishkan). But at the end of two and a third sedras – at the end of the first Aliya of Ki Tisa, we find a "reminder" about Shabbat. Which is not just a reminder, but a connector to the whole idea of Mikdash.
Where as Mikdash is all about the sanctity of PLACE, Shabbat is about the sanctity of TIME. Mikdash and Shabbat are partners. We learn the details of the Melachot from the Mikdash. Other p'sukim highlight this partnership. And after the disaster of the golden calf and its aftermath, the Torah brings us back on track in this week's sedra with the making of the Mishkan – but precedes the whole large Mishkan portion with a three-pasuk reminder of Shabbat. In addition to reiterating that Shabbat must be "kept" and that willful violation is a capital offense, the Torah presents a fifth mitzva about Shabbat – that Sanhedrin cannot execute or otherwise punish someone on Shabbat.
Shabbat and Mikdash are "way up there" in importance and significance in Torah Judaism. Without resorting to arguing which one is higher, let us point out that G-d culminated His Creation of the world with Shabbat, He added a strong Shabbat connection to the Exodus, Shabbat is considered a foretaste of the World to Come, Shabbat is the eternal and everlasting sign of our relationship with G-d. May we merit many Shabbatot, and the rebuilding of the Mikdash in our time