The Reds led 3-0 after 34 minutes with Molyneux firing home from 20 yards on eight minutes after picking up a loose ball in midfield.
The winger doubled Stanley's advantage after 25 minutes when he collected the ball 25 yards out and, with nothing on, rifled it into the roof of the net.
It was three in the 34th minute after Francis Jeffers was clean through and Chiro N'Toko fouled him in the area. Molyneux slotted home the penalty with N'Toko lucky to escape with a yellow card.
Barnet pulled a goal back on the stroke of half-time with Elliott Johnson belting the ball into the roof of the net after a goalmouth scramble.
Ross Jenkins reduced the deficit to one with a spectacular overhead kick from Barry Fuller's 63rd-minute cross.
In a tense finale Edgar Davids saw red after 87 minutes for a second bookable offence, having also been sent off against Stanley at Underhill earlier this season.