Several missed chances cost Paulton, with Cirencester finishing third setting up a home play off semi-final against Winchester City.
Centurion striker, Ben Whitehead, struck wide then had a chance snuffed out by Rovers keeper, Aaron Sainsbury.
Paulton skipper tried to chip visiting keeper Alex Harris from Ed Butcher's free-kick then the visitors responded as Jake Lee headed over from Jake Mawford's corner.
On forty five minutes Cirencester went ahead as Whitehead bore down and shot home, despite his colleague Josh Nelmes blocking the path of defender Martin which went unpunished.
Three minutes into added time from another Mawford corner Whitehead headed home.
From the restart, Lee Ibrahim had a chance to reduce the arrears then Will Harvey narrowly shot over the cross bar and sub Jack Ball saw his drive parried away by Harris.
Paulton pulled a goal back on seventy five minutes as Alfie Clarke and Butcher combined to send Ibrahim down the left and his low cross was turned home by Thomas.
Harvey, Butcher and 17-year-old sub, Kai Williamson all saw chance go wide then Williamson through on goal somehow missed the target.
Harvey found Clarke whose shot was spilled by Harris just out of the range of the on rushing Thomas.
Paulton Rovers player of the match was Will Harvey.
Tony Walsh