Tallying up retail sales from December 28, 2015 to December 25, 2016, Famitsu has revealed that the top-selling game of 2016 in Japan was Pokemon Sun/Moon for Nintendo 3DS, which moved over 3.2 million copies. In 2nd place was Yo-kai Watch 3: Sushi/Tempura for 3DS with 1.4 million sold, and in 3rd was Final Fantasy XV for PS4 with 860,000 sold.
In hardware, 3DS was #1 with 1.87 million units sold, followed by PS4 in 2nd with 1.79 million units sold and PS Vita in 3rd with 865,000 units sold. Compared to 2015, 3DS and PS Vita sales were down, but PS4 sales were up.
According to Famitsu, here’s the best-selling games and systems of 2016 in Japan at retail:
Games (Lifetime)

Pokemon Sun/Moon (3DS) – 3,246,222
Yo-kai Watch 3: Sushi/Tempura (3DS) – 1,397,436 Final Fantasy XV (PS4) – 860,127
Super Mario Maker (3DS) – 743,388
Dragon Quest Monsters Joker 3 (3DS) – 623,083
Yo-kai Sangokushi (3DS) – 563,395
Yo-kai Watch 3: Sukiyaki (3DS) – 509,667
Kirby: Planet Robobot (3DS) – 479,698
Splatoon (Wii U) – 398,251 (1,463,148)
Minecraft: PS Vita Edition (PSV) – 397,607 (876,085)

Systems (Lifetime)

Nintendo 3DS (all models) – 1,874,457 (21,911,413)
PlayStation 4 (including PS4 Pro) – 1,790,883 (3,921,616)
PlayStation Vita (including PS TV) – 865,002 (5,247,419)
Famicom Mini – 567,000
Wii U – 336,151 (3,279,738)
PlayStation 3 – 50,978 (10,257,719)
Xbox One – ...