Latin words/names from the roots *dyḗws and *dʰéǵʰōm
The usual form of the sky god's name in Latin was Iuppiter, or its variant Iūpiter, which pretty obviously goes back to *dyḗws ph₂tḗr. Specifically, Michiel de Vaan says that the Latin nominative/vocative singular form of this name is derived from a vocative phrase, which in PIE would have the form *dyéw ph₂tér (Etymological Dictionary of Latin and the other Italic Languages, 2008). By pretty regular sound changes from PIE to Latin, *dy- became /j/, *ew became /uː/, h₂ between consonants in a non-initial syllable became /i/. The change from original /uːp/ to /upp/ is considered to be part of a sporadic but somewhat widespread phenomenon called the "littera rule".
The standard inflection of Iuppiter as given in grammars includes the ending -piter in the nominative/vocative singular, but not in other cases: that is, forms such as Iovis (genitive singular), Iovem (accusative singular), etc. are used as oblique forms of Iuppiter.
Some less common alternative forms of the nominative singular are attested: De Vaan mentions Diespiter, Dispiter, and Iouis (i.e. Iovis) as attested nominative forms synonymous to Iuppiter.
Proto-Indo-European *dyḗws is reconstructed as having an unusual inflection, and as a result, its inflection was regularized in different ways, yielding both the Latin word Iuppiter meaning "Jupiter" (the name of the sky father) and diēs meaning "day". Dius is a third possible derivative of *dyḗws, coming from the nominative or genitive. This dius is mainly encountered as an adverb meaning "by day"; De Vaan also mentions an expression Diūs Fidius meaning 'god of oaths'.
In my opinion, Iuppiter is the best way to represent *dyḗws ph₂tḗr in Latin (given the constraint of using the same roots). I think alternatives would be less clear. But I guess you can at least say that Diūs pater or Iovis pater would be formed from attested components. I'm not sure how Diūs was inflected outside of the nominative singular (actually, I don't know how De Vaan knows that Diūs Fidius includes this form and not dīus, discussed below), so I'd recommend avoiding that one, at least if you plan to use the name in Latin. And a problem with Iovis is that it is also the genitive form, so Iovis pater could easily be misunderstood as "Jupiter's father" (it is used with this sense by Augustine: "aut de Saturno invenire quo modo et Iovis pater esset et Iovi regnanti subditus factus esset et cetera talia").
Aside from *dyḗws, linguists reconstruct a related Proto-Indo-European word formed on the same stem, *deywós. This also diverged into several forms in Latin: deus, the word meaning "god", dīvus, an archaic or poetic synonym of deus, also used in some cases as an adjective; and dīus, a variant of dīvus where the v was lost before the following rounded vowel. This dius has the same spelling as the one mentioned above (the lines above long vowels are not part of Latin spelling), but a different etymology and a different meaning.
While this second set of words is ultimately related, it is a derivation, so I would say deus pater or dī(v)us pater are hardly any more of an exact match to *dyḗws ph₂tḗr than Iuppiter is.
Humus seems to be the only real option for a Latin noun derived from *dʰéǵʰōm meaning "earth", so assuming you go with this, humus mater seems the best that can be done. I worry somewhat that it might sound as awkward as "mother dirt" or "mother ground" would in English, although the Dictionary of Medieval Latin from British Sources entry for humus (available online at Logeion) indicates the word had at least some eventual use in personifications, including even a case of "mater humus":
3 the Earth; b (personified).
vir hŭmilis maesta caelum conscendit ab hūmo Alcuin Carm. 119. 2; dum nive canet humus, glacies dum cepit aquarum / cursus Walt. Angl. Fab. 10. 1. b plaudit humus, Boree / fugam ridens exulis P. Blois Carm. 7. 1; gaudet mater humus, gaudet et incola / concepta sibi vernula Garl. Poems 1. 3; principio regis oritur transgressio legis / quo fortuna cadit et humus retrogreda vadit Gower CT I 6.
But these examples all seem to be in Christian authors, where this personification is probably not supposed to be considered a goddess. I do not think it is traditional in Classical Latin to use humus as the name of a goddess.
How I would actually translate "sky father" and "earth mother" into Latin
You mentioned wanting to aim for symmetry. But I think there is an unavoidable conflict between that goal, your other stated goal of using "words directly derived from those roots", and a third goal which I assume might have some weight of using terms that actually mean "sky father" and "earth mother" in Latin.
If you want the names to convey the idea of a pair of deities consisting of a masculine personification of the sky and a feminine personification of the earth, then the name Iuppiter is somewhat problematic: although clearly associated with the sky, Juppiter is not really just a personification of the sky in Classical Latin times. And his consort is typically identified as Juno, who I do not think is considered to be an earth goddess.
The Classical Latin word for the sky or heavens was caelum, and the personification of the sky was given the name Caelus in Latin. This name can be paired with Terra or Tellus as a personification of the Earth, to express something like the sense of the Greek deities Uranus and Gaea (Οὐρανός and Γαῖα); accordingly, "Caelus pater" and "Terra/Tellus mater" express something like English "Father Sky" and "Mother Earth".
If instead of actual personifications, you mean something more like "father in/ruling over the sky/heaven(s)" and "mother in/ruling over the earth", I would guess the most effective way to convey that meaning in Latin would probably involve derivatives of caelum and terra/tellus, although I'm not sure exactly what formations would be best.
