The 19-year-old, who is yet to score a competitive goal for the Gunners, put the tourists ahead on 30 minutes with a low finish from 12 yards before slotting home a penalty in the second half.
Jack Wilshere had dispatched a penalty of his own in between Akpom’s first two goals, before the young striker headed into the top corner from six yards to round off a fine performance.
Arsenal will play Everton in the final on Saturday after the Toffees saw off Stoke 5-4 on penalties following a goalless draw earlier on Wednesday in the same stadium. Singapore Select XI face Stoke in the third-place play-off on the same day.
Arsene Wenger kept Petr Cech waiting for his Arsenal debut as Emiliano Martinez started in goal in an XI including Wilshere, Alex Oxlade-Chamberlain and Per Mertesacker, while Wojciech Szczesny was on the bench.
Having been patient early on, Arsenal would have taken the lead on 16 minutes but for a fine a double save from Izwan Mahbud, first denying Alex Iwobi low down to his right before parrying Oxlade-Chamberlain’s ferocious effort from 15 yards.
Akpom put the Londonders ahead after half an hour, finishing a sweeping move from 12 yards after Oxlade-Chamberlain broke with pace.
After the break, Iwobi missed two chances from inside the area, first from Oxlade-Chamberlain’s dinked through ball on the half-volley, and then from Wilshere’s fine cut-back from the right.
But the Gunners doubled their lead on the hour when Mathieu Debuchy was brought down by Sirina Camara on the right of the area and Wilshere stepped up to slam the resulting penalty into the right corner of the net.
Arsenal received another spot kick 14 minutes from time when substitute Jon Toral was cynically brought down by goalkeeper Izwan, Akpom stepping up to send the goalkeeper the wrong way for his second.
And the youngster grabbed his hat-trick late on, heading home Hector Bellerin’s fine cross from six yards.
Akpom nearly grabbed a fourth goal in the last minute, but Izwan did well to parry clear his powerful effort from a slight angle.
Watch Arsenal take on Everton in the Barclays Asia Trophy final on Saturday, live on Sky Sports 1 HD from 1.30pm.