Millwall enjoyed the lion's share of the chances in the opening 45 minutes and comfortably dominated the visitors.
But Hartlepool stunned the New Den six minutes after the break when Anthony Sweeney smashed an unstoppable 20-yard drive beyond Lions keeper Lenny Pidgeley.
The Lions had their chances to find the net early on.
Jamie O'Hara spun Ali Gibb on the left-hand side of the box on 11 minutes, before unleashing a rasping drive which nearly flew through keeper Jan Budtz's legs.
Hartlepool's best chance of the opening period came when an unmarked Ben Clark headed Richie Humphreys' corner straight at the goalkeeper on 14 minutes.
Alan Dunne then wasted Millwall's best opportunity four minutes before half-time when he headed O'Hara's pinpoint corner wide from four yards with not a marker in sight.
Graham Alexander shared his frustration moments later when his header from Ahmet Brkovic's cross was deflected on to the post.
There was little to separate the sides in the second-half's opening exchanges, until Sweeney's stunner put Hartlepool ahead.
But, backed by a boisterous home support, Millwall surged forward in search of an equaliser.
Recent signing Brkovic came close when his fierce shot from close range was cleared off the Hartlepool line by Michael Nelson on 67 minutes.
This was as near as the Lions came and Hartlepool frustrated the home side for much of the second half.
Substitute Ian Moore nearly bagged their second from Richard Barker's ball nine minutes from time.
And their failure to add a second set up a tense finish but Pools clung on.