The Premier League outfit were given a tough test against a Southend side managed by former boss Phil Brown, the man who had led them into the top-flight in 2008, but an upset rarely looked likely.
Michael Timlin did hit the crossbar for the hosts, but Fryatt eventually took centre stage with a 63rd-minute opener, before adding another solo effort in stoppage time.
Bruce told BBC Radio 5Live: "Matty Fryatt got injured in his very first game for me, he was out for 13 months and then went out on loan but since then he's been excellent for me.
"He showed what a good player he is. His second goal was outstanding. I always say, whatever club you are, you are only as good as your strikers.
"We've brought in a couple and it is looking good in that department."
Bruce was particularly happy with the professionalism and attitude of his players at Roots Hall, as Hull progressed to the FA Cup fifth round despite playing in difficult conditions and on a poor pitch.
He added: "The boys showed the right attitude and desire to come away with the win. Through poor conditions, we battled well. As we stand here now it's like hurricane conditions.
"It had all the ingredients for an upset and we had to stand up and be counted. We matched their endeavour, they threw everything at us but that little bit of quality shone through with us.
"I was confident we could make the changes we did today and go through. The players who came in are experienced professionals."
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