Shortly after takeoff, the aircraft transmitted squawk 7700, signalling a general emergency, before switching to 7500, the internationally recognised hijack code.
Israeli officials reported a physical altercation between the two pilots, with one injured, and Flightradar24 data shows the plane plummeted 14,000 feet in under 30 seconds.
Air traffic control rerouted the Boeing 737 MAX 8 to Tabuk, where it touched down safely at 14:55 local time, all 180 on board unharmed.
Flydubai said the aircraft landed safely and has opened a full investigation into the cockpit incident, while Israeli authorities have launched a formal inquiry.
A passenger recalled shouting in the cockpit and said the plane skidded, but was relieved when the crew calmly guided the aircraft to a safe stop.