Having dominated the early proceedings Mathieu Baudry headed Orient ahead on the 21st minute, before Simpson tapped in from close range in first half stoppage time, though Vadaine Oliver was to pull a goal back for The Minstermen just before half time.
Orient were to restore their two-goal advantage on the 64th minute however when Simpson curled home his second of the afternoon, though Oliver pulled a goal back on the 86th minute to set up a nervy ending which saw Orient hold on for all three points.
Ahead of kick-off the O’s announced the signing of French defender Jean-Yves M’Voto, and the Frenchman was one of three changes to the side that lost at Hartlepool, with Alex Cisak and Sammy Moore returning to the side.
In bitter conditions Orient nearly made the breakthrough after only 21 seconds when midfielder Jack Payne took aim from 25-yards, only to see his shot crash back off the crossbar.
Two minutes later Sammy Moore then blazed an effort over from inside the area as the hosts continued to rack up the early pressure.
With the chances continuing to be created Jay Simpson then looked have given Orient an eighth minute lead when he took several touches to work some space in the box but despite his shot beating York goalkeeper Scott Flinders defender Eddie Nolan was there to clear off the line.
Having come close on a number of occasions Orient then took the lead on the 21st minute when Mathieu Baudry got on the end of Moore’s corner to crash a header beyond Flinders.
That was the be the O’s skipper’s final piece of action however as four minutes later he was forced off with an injury suffered, resulting in Cole Kpekawa being handed his debut to partner Jean-Yves M’Voto in the centre of defence.
As the half wore on it was the hosts who continued to press forward, though no clear-cut chances were forthcoming until the second minute of stoppage time when Jay Simpson doubled the O’s lead with a simple finish following a mesmeric run from John Marquis.
The two-goal was not to last however as York managed to pull a goal back seconds before half-time when Vadaine Oliver’s shot from the edge of the box took a heavy deflection to beat Alex Cisak who had been untroubled in the goal.
Following the interval Simpson sent a shot wide in the opening minute but it was York who came the closest when Bryn Morris curled an effort over from 18-yards.
With just over 25 minutes remaining Orient then restored their two-goal advantage when Simpson curled an effort from the edge of the area beyond Flinders to claim his 13th of the season.
Much like the first half Cisak had been rarely tested in the Orient goal but on the 73rd minute produced a splendid save to somehow tip Oliver’s header round the post.
Refusing to give up York then pulled a goal back with four minutes left to play when Oliver sent a header beyond Cisak to set up a tense final few minutes.
Oliver then had a chance to equalise three minutes into stoppage time but could only head straight at Cisak as the O's held on for victory.
ORIENT: Cisak, Clohessy, Baudry (C) (Kpekawa 25), M’Voto, Shaw, Pritchard (McAnuff 82), Payne, Moore, Marquis (Turgott 82), Simpson, Palmer
SUBS: Sargeant, Dunne, James, Kashket
GOALS: Baudry (21), Simpson (45+2 & 64)
BOOKINGS: Moore (50)
YORK: Flinders, Nolan, Swan, Boyle, Ilesanmi, Greening (Sinclair 56), Godfrey (Tutonda 56), Coulson (C) (Straker 80), Morris, Berrett, Oliver
SUBS: Ingham, Straker, Hyde, Collins, Turner
GOALS: Oliver (45+4 & 86)
BOOKINGS: Berrett (37), Boyle (42), Morris (83)
REFEREE: Lee Collins
ATTENDANCE: 4,897 (581)