High winds, a sandstorm and thunder and lightning brought proceedings to a halt, with Japanese rider Nakagami remaining on top overall following his lap in 2m 00.187s on Saturday – the only full day of the final test after Friday's sessions were halted by rain at the desert circuit.
The Idemitsu Honda Team Asia rider only 0.053s ahead of EG 0,0 Marc VDS contender Franco Morbidelli, who was fastest on Sunday after lapping in 2m 00.971s.
Alex Marquez, the2014 Moto3 world champion, held station in third on the combined times on the second of the Marc VDS Kalex machines, 0.240s off the top spot.
Hafizh Syahrin (Petronas Raceline Malaysia) was fourth fastest, half a second back, while Miguel Oliveira kept the new KTM chassis in the top five for Red Bull KTM Ajo, lapping in 2m 00.861s.
Tom Lüthi (CarXpert Interwetten) was sixth overall ahead of rookie Fabio Quartararo (Pons HP 40) impressing in seventh, while Xavi Vierge (Tech 3 Racing) was eighth on the Tech 3 chassis ahead of Britain's Danny Kent, who finished as the leading Suter for Kiefer Racing.
Axel Pons finalised the top 10 for RW Racing, a mere 0.016s behind 2015 Moto3 world champion Kent.
The weather-hampered final test in Qatar brings the curtain down on pre-season for the intermediate class, with the next action taking place on Thursday with FP1 as the first round of the 2017 world championship at Losail gets under way.