The lowest ranked team in the competition came into the clash full of optimism after overcoming Aldershot to reach the first round proper, but in truth the part-timers never looked like causing another upset.
Jennison Myrie-Williams settled any early nerves by finishing well when picked out in space after just 15 minutes.
And from that moment on the visitors were firmly in control of proceedings, and doubled their lead after Chris Birchall tapped in, reacting quickest to Shortwood goalkeeper Rich King's save.
The Southern League Division One South side did come out after the interval with added impetus, but never really created any clear-cut opportunities.
And that proved costly as a Myrie-Williams penalty, given for a John Coates handball, and a stoppage-time Chris Lines header made sure that the Valiants progressed.
Salisbury await the victors, but the non-league side can be proud of their efforts against League One opposition.