Salisbury opened the scoring on 13 minutes as Lewis Benson shot looked to have been finally turned home by Sam Roberts in an offside position. Rovers protest led to assistant manager Paul Tovey been sent to the stands.
Paulton levelled on 20 minute after they were lucky to be awarded a free kick on the right and Josh Ford headed home with the help of the post.
Salisbury captain Kane O'Keefe turned on 35 minutes to hit a tremendous unstable shot from 30 yards out.
Referee Dale Wootton pulled a hamstring and had to be replaced.
O'Keefe missed numerous chances in the second half and his side were to rue as Rovers sub Liam Monelle was fouled in the box and James Byrne equalised from a 75th minute penalty.
Paulton secured the win as Josh Morgan Williams broke and from the edge of the box chipped the ball in for the winner.
Rovers face Cirencester Town at home in the next round to be played on Saturday 28 October K-O 3-00 p.m.
Entertainment Value 3 out of 5
Star man of match - Josh Morgan- Williams (Paulton Rovers)
Attendance 541