Adam's Reed goal inside the opening two minutes put York on their way before Matty Blair got the crucial strike just before the break.
The Minstermen now go into next weekend's trip to Dagenham needing a point to guarantee their League Two status for another season.
"It was a battling performance and you've got to show character and that side of the game and we got that into our play," he said.
"We had to keep going for the 90 minutes and Chris Smith cleared one off the line at the end. It's important we do the right things and credit to the players they're doing what we ask.
"It was a fantastic start. It was difficult conditions with the pitch as it was very dry and bobbly but we managed that as well as we could. We got the result over the course of the game that we deserved.
"It was important that we upped the energy in the second half, we were about a yard off Southend in the first half, and we stepped onto them a bit more in the second half. We've carried it out and it's paid off for us."