Which was the first doctor, M.D. or Ph.D.?
Doctor is a Latin word, and it was borrowed from Latin already formed, with a meaning, namely 'teacher'. The word is formed exactly the way teacher is:
- a verb root (English teach-, Latin doc-), plus
- an agentive suffix (English -er, Latin -tor).
Doctor was in use for many centuries before there were universities, or degrees. It was used to refer to an especially learned person, one who was authorized and qualified to teach a particular subject. Which might be medicine, philosophy, theology, law, logic, history, etc.
It wasn't until the Twelfth Century AD in Europe that the modern Western universities were invented. The first universities were Guilds, of Masters or Students, and the Masters were Doctors, i.e, authorized teachers. Gradually the Bachelor's, Master's, and Doctor's degrees evolved from a guild structure of Apprentice, Journeyman, and Master.
For details, consult Haskins' classic The Renaissance of the Twelfth Century
As noted in etymonline and in previous answer, the word doctor has been in use in English since ca. 1300. Regarding the abbreviations you ask about, etymonline says:
- M.D., "1755, abbreviation of Latin Medicinæ Doctor "doctor of medicine."
- Ph.D, "attested from 1869; abbreviation of L. Philosophiae Doctor 'Doctor of Philosophy.'"
The abbreviations D.D. or similar for Doctor of Divinity and L.L.D. for Legum Doctor or Doctor of Laws are somewhat older than M.D. or Ph.D.. For example, the 21st edition of Nathan Bailey's An universal etymological English dictionary, printed in 1675, shows T.D. in the entry after fifth SYZYGIA entry, and shows L.L.D. after LIZEN'D. 
The answer to "Which of Ph.D. or M.D. was first referred to as a doctor?" is that neither was first, as both D.D. and L.L.D. are earlier.
It seems that doctor for both PhD and MD came about the same time: late 14c ... slowly besteading the OE word for a physician: leech.
From Etymology Online:
doctor (n.) c.1300, "Church father", from O.Fr. doctour, from M.L. doctor "religious teacher, adviser, scholar", in classical L. "teacher", agent noun from docere "to show, teach, cause to know", originally "make to appear right," causative of decere "be seemly, fitting" (see decent). Meaning "holder of highest degree in university" is first found late 14c.; as is that of "medical professional" (replacing native leech), though this was not common till late 16c. The transitional stage is exemplified in Chaucer’s Doctor of phesike (Latin physica came to be used extensively in M.L. for medicina). Similar usage of the equivalent of doctor is colloquial in most European languages ...
In OE and ME, a doctor was a leech (lǣce in OE) which gave us many other words:
leechbook — book of prescriptions
leechcraft — art of healing; medicament, remedy, prescription
leechcraftig (leechcrafty) — skilled in medicine
leechchest — medicine chest
leechdom — medicament, medicine; salvation
leechdomlic — salutary, beneficial, health-giving
leechdomness — cataplasm, poultice
leechfee — doctor's fee
leechfinger — fourth finger
leechhouse — sick room, hospital
leechiren — surgeon's knife, lancet
leechsalve — medicinal ointment
leechseax — lancet
leechwyrt (leechwort) — medicinal herb, drug