Allister Hogg, Euan Murray and Henderson touched down as the Scots appeared to be coasting to the morale-boosting victory they sought with the tournament in France fast approaching.
With Ireland's pack crumbling in the tight and at set pieces - their scrum was particularly woeful - Frank Hadden's side were in full control until the visitors burst into life early in the second half.
Isaac Boss started the revival, Andrew Trimble added a second try and the boot of Paddy Wallace made further inroads into the deficit before man of the match Henderson killed off the game with the decisive try seven minutes from time.
Hadden had selected a near full-strength side in the hope of building winning momentum heading into the World Cup and was rewarded with an enthusiastic display led by the pack.
The experiment of installing Chris Paterson at fly-half was undermined by the wet conditions but the Gloucester back looked at ease and warrants perseverance in the position.
For Ireland boss Eddie O'Sullivan the match was a last chance to see a handful of players in action before finalising his 30-man World Cup squad, which will be unveiled tomorrow morning.
But the soul searching will probably continue long into the night as today's lacklustre display will have provided few extra clues on which of the tight calls deserve a ticket to France.
Munster winger Brian Carney, who converted from rugby league less than six months ago, probably just edged Ulster rival Tommy Bowe in the shoot-out for the last available back three spot.
Carney's greater appetite for work may count in his favour but in the back row, where the competition for places is at its fiercest, O'Sullivan will be none the wiser.