Learn Turkish: İki saattir hâlâ bekliyorum. - I am still waiting after two hours.

The suffix -DIr is used to show duration, meaning "for [a period of time]". So, iki saattir literally means "for two hours." The sentence literally says "For two hours I am still waiting," which the translation smooths out to "I am still waiting after two hours."

The last vowel in saat is a. Shouldn't vowel harmony make the suffix -tır instead of -tir?

Normally, yes! However, saat is an Arabic loanword and is one of the most famous exceptions to Turkish vowel harmony. Suffixes attached to saat act as if its final vowel is a front vowel (like e or i). That's why it takes -tir instead of -tır, just like it pluralizes as saatler instead of saatlar.

Why does the suffix start with t (-tir) instead of d (-dir)?

This is due to consonant assimilation (the "Fıstıkçı Şahap" rule). The word saat ends in t, which is a hard (voiceless) consonant. When a suffix starting with d attaches to a hard consonant, the d changes to a t to match it smoothly.

English uses "I have been waiting" here. Why does Turkish just use the present continuous tense bekliyorum ("I am waiting")?