Second half goals from Idris Kanu and Harry Pritchard were enough to move the Bees up into seventh as David Unsworth's Latics dropped to 21st.
Unsworth had promised changes after their last league game, and he handed league debuts to three players, including returning defender Peter Clarke, the 40-year-old defender who is back for a second spell at the club.
But there was a familiar feeling when Kanu broke the deadlock in the 57th minute, scoring from a tight angle.
Ben Tollitt was denied a leveller by Bees goalkeeper Laurie Walker, before Pritchard then made certain of a third straight win on the road for Barnet with three minutes to go.
"It's just difficult, but we've got to keep going," said Unsworth.
"We've got to stick together.
"It's a long season and we've got to pick ourselves up and go again."
Latics' next three games are all away from home, starting this Saturday with a trip to Maidstone.
