
Rabbi Dr. David M. answered 02/16/21
Bible Professor w/ 10+ yrs teaching Biblical Hebrew
This is an excellent, high-level question. The vowel change between יאֹמַר and וַַיּאֹמֶר is due to a shift in stress. In יאֹמַר the stress is at the end of the word, hence the long patach, but when we lengthen it to וַַיּאֹמֶר the stress is moved up a syllable. This shift causes vowel reduction. What makes this particular case unique is the guttural-like ר at the end of the word. This letter prefers a segol for vowel reduction, hence verbs like וַיָצֶר and nouns like בֹּקֶר. So, when a ר is involved the reduced vowel becomes a segol.
For the two principles I mentioned see "A Grammar of Biblical Hebrew" (Jouon-Muraoka) §23b and §73d-e.