Burton's relegation fears were exacerbated after defeat at Morecambe.
Chris McGready bundled in James Spencer's volley from close range to give the hosts the lead.
Jacques Maghoma twice fired wide when well-placed for an equaliser before Danny Carlton smashed in to double the Shrimps' advantage.
The visitors came back strongly and pulled a goal back when Maghoma slotted under keeper Barry Roche, but then saw Sam Winnall's late effort fly wide.
Burton are now level on points with 23rd-placed Barnet, albeit with two games in hand over the Bees.
Morecambe remain in 15th position in the League Two table.
Burton Albion manager Paul Peschisolido told BBC Radio Derby:"It's not good is it? If we defend like that, we've got no chance.
"Long balls through the middle killed us today. We do it every week. Every week, one long ball. We did it last season, we're doing it this season and it's killing us.
"We've tried every combination and everyone does the same, regardless of who we put in there. We keep working on it but we can't deal with it so we have to keep working on it, I guess.