The Minstermen, who are now two points above the drop zone, made the perfect start inside the opening two minutes with midfielder Adam Reed scoring after a deflection in the area fell kindly to him to beat Daniel Bentley.
Fifteen minutes after the opening strike, Southend tested Michael Ingham for the first time but Barry Corr's header proved to be no trouble for the goalkeeper.
In the 22nd minute the Shrimpers restored parity through Ryan Leonard with the midfielder glancing home a horrible miscued clearance from Jack O'Connell.
The scores were not level for long as York regained the lead five minutes before the break as Matty Blair blasted home Tom Platt's pass from inside the area.
Chances were at a premium for both sides in the second half with both Blair and Platt going close for York. Southend thought they had grabbed a point at the end but Gavin Tomlin's goal was ruled out for offside.