Popovic enjoyed the perfect start to his tenure in the Turkish top tier posting a hard-fought 1-0 win over fifth-placed Kayserispor in the Super Lig to break the side's five-game winless run in his first game at the helm last week.
But he couldn't back the victory up on Saturday night.
Popovic's side had lost two players through suspension - Paul Papp and Ceyhun Gülselam - for the match against Osmanlispor, who posted just their second win in nine games so far this season.
Three second-half goals ensured the victory for Osmanlispor with Portuguese import Tiago Pinto opening the scoring just after the hour mark as French attacker Serdar Gurler netted a brace to round out the win.
Karabukspor, sitting just above the relegation zone in 15th spot on the ladder, face another tough test next week when they face ninth-placed Sivasspor.