Superlative of a different stem
In present-day English, best sits at the top of two everyday scales. As an adjective it is the superlative of good: most excellent, most suitable, or, in a looser use, the greatest share of something, as in the best part of an hour. As an adverb it is the superlative of well. As a noun it can mean the finest example, the utmost a person can do, or a set of formal clothes. As a verb, from the mid-nineteenth century, it can mean to outdo someone. None of that ranking is built on the word good. The origin of the word best belongs to another Germanic family that English kept for the comparative and the superlative after it had replaced the old positive grade.
Inherited, not borrowed
The word is native. It is already in Old English, in the period before 1150, in spellings such as betst, betest, and bezt. The cluster in betst was clumsy in the mouth; the middle consonant faded by assimilation, giving beste and then the modern form. In those early texts it is already both an adjective, of the highest quality or standing, and an adverb, in the most excellent manner. Late Old English also uses it for what is most advantageous or most fitting.
The same superlative runs through the old Germanic languages: Old Frisian and Old Saxon best, Middle Dutch best, Old High German bezzist, modern German beste, Old Norse beztr, Gothic batists. Living cousins include Dutch best, Danish bedst, Swedish bäst, Norwegian best, Icelandic bestur, and Scots best. That map is the mark of inheritance from a common ancestor, not of a later loan into English.
The unused positive
Reconstructed Proto-Germanic has a superlative *batistaz, made with the ordinary superlative suffix *-istaz on a stem *batiz-. The matching comparative *batizô is the source of English better, German besser, Dutch beter, Gothic batiza, and their kin. Behind them sits a reconstructed positive *bataz, with a sense close to good. Whether that positive was still a living adjective in Proto-Germanic is unclear: it left no secure descendants as a plain word for good. What did survive were the comparative, the superlative, and a group of related nouns and verbs.
English filled the empty positive slot with good, from a separate Proto-Germanic adjective *gōdaz. The result is a mixed set: good, better, best. The adverbial side does the same thing with well, better, best. German gut, besser, beste and Dutch goed, beter, best show that the pairing is old in the family, not an English invention.
A related noun is Old English bōt, meaning remedy, reparation, help, or advantage, from Proto-Germanic *bōtō. Some accounts treat best as historically the superlative that belonged with that noun; others treat the adjective forms and the noun as sister growths on the same root *bat-. Either description is compatible with the evidence. The simple noun barely survives in English. Its last ordinary home is the phrase to boot, from Old English to bote, meaning as an extra advantage. The word for footwear that looks identical comes from Old French and is a different history.
How far the root can be pushed
Beyond Germanic the trail thins out. Some dictionaries reconstruct a Proto-Indo-European root of the *bhad- or *bʰed- type, glossed as good or as improve, and some comparative work links that root with Sanskrit bhadra, fortunate or excellent, and with a Celtic group around Welsh bodd, pleasure. Other specialists in Germanic etymology find no convincing Indo-European source at all. The disagreement is worth leaving open. The Germanic comparative and superlative are solid; the deeper root is a hypothesis.
Once that history is in view, the English shape is plain. The -st of best is the old superlative ending, the same family of ending that yields -est in newest or oldest. The first part is not the word good and not a prefix. It is the *bat- stem. Splits that try to read the word as be- plus some other piece are folk etymology.
Senses that accumulated later
The core ranking sense is already Old English. What changes afterward is mostly specialization and new parts of speech.
By about 1200 the adjective has a matching noun: that which is best. Around 1300 that noun can mean all that a person can do, the sense still alive in do one's best. By the 1570s it can mean the highest state one reaches; by 1790 it can mean one's finest clothes. Fixed phrases gather in Middle and Early Modern English: at best from the early fourteenth century, for the best from the late fourteenth, make the best of from the 1620s, get or have the best of from the 1640s.
Social compounds show how ordinary the word had become. A best friend is already in Chaucer in the late fourteenth century. Best man, for the groom's chief attendant, is recorded in 1814 from Scottish usage, taking over from groomsman. Best-seller, first as a trade shortening of best-selling book, appears in 1889. The verb to best someone, to get the better of them, is attested from 1863.
One Middle English competitor faded. The short form bet, used as an adverb and sometimes as an adjective, stood beside better and best. By about 1600 it had been pushed out. English kept the longer comparative and the superlative and let the stub go.
A fossil in a bargain phrase
The useful reminder is not that best means most good. It is that English still carries a scrap of the older family in a phrase that looks like clothing for the feet. When something is thrown in to boot, the extra is an advantage in the old sense of bōt, the same root that supplied better and best after the everyday adjective for good had been replaced. The ranking words did not grow out of good. They grew out of a stem that English otherwise almost abandoned.