The first of many set-pieces for the visitors almost reaped rewards after 11 minutes, when Paul Brooker's corner was met by Ed Hutchinson's downward header, but the ball flew over after deflecting off Paynter's boot.
Brentford missed out again soon after when DJ Campbell's winding run to the by-line produced a cross that unfortunately fell behind Lloyd Owusu's attacking run.
As time went on Paynter's increasing contribution caused the Bees no end of problems and he threatened twice towards the end of the first half.
Another long ball, this time from Mark Innes put the young Vale striker through on goal but a tight angle forced his shot wide.
Visiting shot-stopper Stuart Nelson was finally tested properly after 36 minutes when Paynter squeezed through the defence, but the goalkeeper's quick reactions stopped him in his tracks.
However, it was Nelson's 53rd-minute error that gifted Vale the lead, as Michael Cummins' 25-yard shot slipped under his body.
Cummins almost doubled the home side's advantage six minutes later when he cut in from the right of the box, but his left-footed strike missed the target.
Bees boss Martin Allen's frustration boiled over 20 minutes from the end when his reaction to a Lowndes tackle earned him a seat in the stands.
Home nerves were rattled on 81 minutes when Kevin O'Connor was given a clear opportunity to shoot from the right of the box but hammered his effort into the side netting.
Four minutes of added time were gifted to the visitors and despite a disallowed goal, Vale hung on to claim the points.