Nagashima grabbed the lead late on and opened up an insurmountable gap to cruise to his first win, some 10 years after fellow Japanese rider Shoya Tomizawa won the very first Moto2 race in Qatar.
Valentino Rossi protege Luca Marini grabbed the holeshot from second on the grid on his Sky VR46 Kalex, with poleman Joe Roberts losing out to Italtrans’ Enea Bastianini at Turn 1.
Bastianini came through to take the lead at Turn 12, though was quickly repassed by Marini on the run into the first corner on lap two.
A moment for American Racing Team rider Roberts at Turn 1 early on left him with work to do to get back into the podium places, but he got himself in a position to attack Marini at the start of lap seven.
However, he ran wide and allowed the VR46 bike back through, with Marini using the grip of his supersoft front tyre to build up a gap of eight tenths by lap 11.
He managed to eke this out to close to a second, but the chasing pack started to reel him in, with Roberts coming through at the last corner on lap 15.
Pons’ Lorenzo Baldassarri also saw his opportunity and tried to pass the pair of them at the same time, but ran in too deep.
But the ex-VR46 Academy member managed to get his hooks into Roberts and scythed past at Turn 6, while Marini’s pace dramatically fell into a void as his front rubber had cried enough.
All this battling allowed Ajo’s new signing Nagashima to get into podium contention, before he launched a daring raid into Turn 1 on lap 18 and fended off Baldassarri’s retaliation.
Nagashima subsequently pulled the pin and went onto the final lap 1.2 seconds clear of the field – a gap he would not relinquish through to the chequered flag.
Baldassarri held onto second for his first podium since he won last year’s Jerez race, ending a barren period for the Pons rider, while Bastianini completed the podium.
Roberts was denied a maiden podium by 0.131s in fourth ahead of Remy Gardner – who is still on last year’s Kalex chassis in SAG colours – and a late-charging Jorge Navarro on the Speed Up.
Marcel Schrotter lifted himself up from 13th on the Intact GP Kalex to end the night seventh, with Aron Canet (Aspar Team) a strong eighth on his Moto2 debut.
Petronas Sprinta’s Xavi Vierge and Tom Luthi on the sister Intact bike rounding out the top 10.
Marini dropped to the fringes of the points on the last lap, but would not see the chequered flag after contact with Jake Dixon (Petronas Sprinta) took him out at the last corner.