Jim Magilton's side were saved from a drubbing by the acrobatics of Richard Wright and some poor United finishing after the interval as the visitors fell apart.
United, whose undefeated run in March earned Kevin Blackwell the manager of the month award, forced the early pressure.
Wright pulled off a brave save after Greg Halford's long ball upfield unlocked the Ipswich defence.
Henderson closed in at the near post only to be stopped by the former England keeper as he dived bravely at the feet of the big striker.
But Wright was helpless in the 19th minute as Halford unleashed an unstoppable shot from 25 yards.
His right-foot strike powered into the far corner beyond the helpless keeper for his seventh of the season.
As the Ipswich back four went into panic mode the Sheffield side pushed further ahead in the 27th minute.
David Cotterill's cross into the area caused problems and the ball was only half cleared to Kyle Naughton, whose precise cross was headed over the line in clinical fashion by Henderson.
Wright produced another stunning save as United sensed it could be there day after diving to fingertip Cotterill's swerving cross from the left flank round the foot of the post.
Ipswich stood flat-footed again as Halford served up another of his trademark long throws.
The ball reached the unmarked Jamie Ward - the smallest player on the field - and his header grazed the foot of the post with Wright beaten.
Ipswich were handed a rare opportunity when Paddy Kenny only half cleared a cross from the left flank but midfielder Owen Garvan slammed the ball into the side-netting from 15 yards.
Ward had a chance to grab a third goal as the former Chesterfield striker wriggled past two challenges to the edge of the area only to drag his low shot wide of the target.
Henderson, in search of his eighth goal of the season, should have killed off Ipswich after Halford had done the hard work but steered a tame header straight into Wright's waiting hands.