A forwards-dominated first half ended 13-6 in Scotland's favour, Johnny McPhillips' brace of penalties keeping Ireland in touch after leaking an early Cameron Hutchison try.
Hooker Tadgh McElroy's try off the back of a 42nd minute lineout maul had Nigel Carolan's youngsters level, but the Scottish pack got on top again to see out-half Henderson add two more penalty goals for a 19-13 lead.
Much to their credit, the Ireland forwards, including tireless carriers Caelan Doris and Cillian Gallagher, were clinical from their only remaining scoring opportunity, wearing down the home defence for Boyle to strike from close range.
Number 10 and man-of-the-match McPhillips, whose kicking out of hand had kept his side in the hunt, nailed the conversion. Henderson was narrowly wide with his long range shot at glory, and lock Oisin Dowling's crunching tackle, which forced a knock-on, allowed Ireland to control possession up to the final whistle.
After a delayed kick-off due to a technical fault between the match officials, Ireland had the advantage of a decent wind in increasingly cold conditions in Cumbernauld. The visitors only had two players back from last year compared to Scotland's eight.
Scottish out-half Henderson dropped a testing fifth-minute penalty short after UL Bohemians prop Joey Conway was pinged at the second scrum. The hosts maintained the early pressure and after mauling up close from a lineout, centre Hutchison took a hard line to bulldoze over from a few metres out.
Henderson's conversion was cancelled out by McPhillips' first three-pointer of the night, Ireland steadying the ship after McElroy was pinged for a dummy lineout throw and number 8 Doris was guilty of holding on following a midfield carry.
The Irish eight, including returning flanker Gallagher, carried strongly in the lead up to McPhillips' second penalty goal towards the end of the first quarter, cutting the gap to 7-6.
However, Scotland's very effective maul and scrum gave them a considerable advantage as the first half wore on. Possession-starved wingers Jordan Larmour and Colm Hogan reacted swiftly to deny Darcy Graham in the left corner after new Irish captain Jack Kelly had failed to deal sufficiently with a cross-field kick.
The Scots kept up their stranglehold of possession and territory, earning a 39th minute penalty shot for Henderson which he duly slotted for a 13-6 interval advantage.
Ireland's brave decision to go for the corner almost immediately on the resumption was rewarded. The Scottish defence struggled to contain a well-executed maul and Lansdowne clubman McElroy rumbled over for McPhillips to land the levelling conversion.
Sean Lineen's charges turned the screw once more via their strong set piece, exerting further territorial pressure for two more crisp strikes from Henderson. Ireland also had to cope with the departure of full-back and skipper Kelly who damaged his shoulder in contesting a high ball.
At 19-13 down, Ciaran Frawley provided the inspiration for Ireland with a jinking midfield run and a subsequent penalty was dispatched to touch. Although the chance was lost due to McElroy's crooked throw, a good touchfinder from Hogan and two very important tackles from McPhillips saw Ireland bounce back into an attacking position.
They needed no second invitation as an exhaustive bout of carrying from the forwards, with Fineen Wycherley, Dowling, the talismanic Gallagher and Doris all to the fore, ended with Boyle's all-important try to the left of the posts.
And it was Ireland who held their nerve when it mattered most, Ulster 'A' starlet McPhillips converting into the difficult wind, a resilient defence halting Scotland in their tracks and then a slice of good fortune seeing Henderson make a rare error off the tee.
TIME LINE: 5 minutes - Scotland penalty: missed by Josh Henderson - 0-0; 8 mins - Scotland try: Cameron Hutchison - 5-0; conversion: Josh Henderson - 7-0; 15 mins - Ireland penalty: Johnny McPhillips - 7-3; 21 mins - Ireland penalty: Johnny McPhillips - 7-6; 26 mins - Scotland penalty: Josh Henderson - 10-6; 39 mins - Scotland penalty: Josh Henderson - 13-6; Half-time - Scotland 13 Ireland 6; 42 mins - Ireland try: Tadgh McElroy - 13-11; conversion: Johnny McPhillips - 13-13; 54 mins - Scotland penalty: Josh Henderson - 16-13; 63 mins - Scotland penalty: Josh Henderson - 19-13; 72 mins - Ireland try: Paul Boyle - 19-18; conversion: Johnny McPhillips - 19-20; 78 mins - Scotland penalty: missed by Josh Henderson - 19-20; Full-time - Scotland 19 Ireland 20
Referee: Christophe Ridley (England)