Fryatt's second-half double proved enough for victory at Roots Hall over former Tigers manager Phil Brown.
Tigers boss Steve Bruce said: "I would not expect a team of mine to roll over just because we are coming here in the cup, so they showed the right desire and attitude.
"The pitch was difficult, and towards the end it was awful conditions, a typical cup tie, sometimes in football you have to roll up your sleeves and we did that in abundance today to get through."
Bruce feels the competition offers him the chance to fully utilise the squad.
He said: "Somebody like Matty Fryatt, if I don't give him an opportunity to play, then they are knocking down the door.
"Matty had come back into the side today and reminded me what a good player he is.
"I was confident we could come here and make the changes, they are all experienced players - Abdoulaye Faye, (Paul) McShane, Meyler, (Stephen) Quinn, (George) Boyd, Matty Fryatt, Danny Graham, and we should be good enough if we do it right to get through and I had big belief we would do that."
For breaking stories and all the great banter like us on Facebook: facebook.com/tribalfootball