McIntosh, out since August with a knee injury, returned to first-team action and nearly stole the points with a bullet header from fellow substitute Adnan Ahmed's free-kick whipped in from the right.
But Flahavan, who had little to do all game, stayed alert and pulled off a great save by tipping the ball over the bar at full stretch.
It was the closest either side came to scoring in an encounter, where there was plenty of flowing passing of football to admire, but few clear cut chances.
Huddersfield needed 79 minutes to get an effort on target - but veteran striker Andy Booth's header from Pawel Abbot's by-line cross was saved by Flahavan.
Injury-hit Southend's best chance came on 66 minutes when Jay Smith put Mark Gower through only for keeper Paul Rahubka to beat out his low shot with a neat parry.
Smith, back in action after 18 months on the treatment table, went off with a hamstring injury soon after that will require more attention form the physio.
That blow came on top of a pre-match setback for 10-goal top scorer Freddy Eastwood. He had been expected to play, despite picking up a calf strain in the 1-1 draw with Bradford last week, but failed a fitness test.
Eastwood's predatory instincts were missed and Southend instead concentrated on restricting the number of chances that the home side could create.
The Shrimpers have still to beat Huddersfield in the competition. The Essex club have lost 4 and now drawn 4 from just 8 meetings between the sides in total, and they never really looked like breaking their duck today.