Despite dominating for long periods, the Premier League side were unable to find a breakthrough against their League Two opponents at Victoria Park during the first half.
But the mass introduction of youth-team prospects after the break turned the game in the Premier League side's favour, with head coach Gus Poyet electing to change his entire starting XI early in the second period.
The decision paid dividends as Carl Lawson's strike and a double from Under-21 team-mate Andrew Cartwright sealed victory.
The result came just 24 hours after a 1-0 success at Carlisle United.
Poyet rung the changes shortly after the interval, and the introduction of fresh legs had the desired impact with three second-half goals.
Striker Lawson broke the deadlock in the 70th minute, curling into the bottom corner following a one-two on the edge of the area with Mikael Mandron.
Defender Cartwright then doubled the advantage two minutes later before putting the game beyond doubt with a deflected third in the 78th minute.
