Trabzonspor broke open the scoring when Abdulkadir Omur hit a powerful left-foot shot from close range in the 48th minute on a snow-covered field at Caykur Didi stadium.
Finnish striker Pohjanpalo converted two penalties in the 59th and 64th minutes to put his team ahead. But the Black Sea side leveled with Djaniy in the 70th minute.
Pohjanpalo scored again on a penalty kick in the fifth minute of second-half stoppage time to give Caykur Rizespor the home victory.
It was the second Super League defeat for Trabzonspor, whose 13-match unbeaten run came to the end.
Despite the loss, Trabzonspor are atop the standings with 70 points. Caykur Rizespor are in the 19th spot with 26 points.