The Gulls, 2-1 winners over Chesterfield on Tuesday, got off to another flying start and again led 2-0 at half-time, pressing from the start before duly taking a sixth-minute lead.
Skipper Lee Mansell sent in a corner and on-loan Sheffield United winger Jordan Chapell fired the ball back into the area as York failed to clear their lines and there was Elliot Benyon, scoring on the spin from eight yards.
It was the Southend striker's first goal since rejoining his former club on loan over a month ago.
Torquay forged further ahead in the 23rd minute when forward Ryan Jarvis finished off a surging run from the halfway line with a brilliant left-footed drive into the roof of the net from 20 yards.
York started the second half brighter, Josh Carson shooting just wide on a sweeping counter-attack after 52 minutes.
City did pull a goal back in the 72nd minute through new loan striker Richard Cresswell, his penalty coming after Thomas Cruise was sent off for fouling Carson as he prepared to left fly from just inside the box. But it was not enough to snatch a share of the spoils.