The Initial Upper Paleolithic (IUP) is a key chrono-cultural concept in our understanding of the cultural and population dynamics at the transition from the Middle Paleolithic to Upper Paleolithic period. This paper presents technological and chronological analyses of lithic assemblages from a rockshelter site at Tor Fawaz in the Jebel Qalkha area, southern Jordan, to provide accurate dating and detailed recognition of the IUP variability in the Levant. We present integrated micromorphological, phytolith, and dung spherulite analyses to evaluate formation and postdepositional processes of archaeological remains through high-resolution micro-contextual studies. As a result, the Tor Fawaz assemblages show general similarity to those of Boker Tachtit Level 4, Tor Sadaf A–B, and Wadi Aghar C–D1 that represent the late phase of the IUP in the southern Levant. Based on the detailed recognition of site-formation processes, we suggest ca. 45–36 ka as the age of IUP occupations at Tor Fawaz. More specifically, the IUP occupations at Tor Fawaz and Wadi Aghar, a nearby IUP site in the same area, may represent slightly different phases that show a lithic technological trend paralleling the IUP sequence at Tor Sadaf in southern Jordan, and possibly post-date Boker Tachtit Level 4. We also discuss the issue of partial chronological overlap between the late IUP and the Ahmarian and also argue for the geographically different trends in cultural changes from the late IUP to the Ahmarian.