Late goals by Dungannon duo Ryan Harpur and Paul McElroy consigned pointless Ballymena to a fourth consecutive defeat in the Irish Premiership.
Glenn Ferguson's United had been the better team for much of the Stangmore Park contest before a late collapse saw Dungannon bag all the points.
Harpur beat the offside trap and got the better of keeper Dwayne Nelson for the breakthrough goal on 78 minutes.
Near the end McElroy made it 2-0 with a sweetly-struck shot.
"When you are down at the foot of the table, football can be a harsh game," said United manager Ferguson.
"I thought we deserved something from the game. We had more attempts than they did and our keeper did not have many saves to make.
"But if you do not take your opportunities you can get punished.
"That's what happened. It is our responsibility and we have to look at that.
"I was really happy with the way the boys went about it today. They showed hunger and commitment."