The Sunderland striker's first goal in four matches coincided with the province's first victory in Group 3. It was also their biggest win in 13 years.
It was a comfortable one at that, although they had to wait until the 30th minute before Healy made the breakthrough.
Northern Ireland grew in confidence after the opener, though, with Grant McCann, Kyle Lafferty and Steven Davis all finding the target to add gloss to the scoreline.
They should have been ahead as early as the third minute when Michael O'Connor, making his first start, headed over from close range following a cross from Davis.
The province set a high tempo from the off and Keith Gillespie rattled in a shot after 10 minutes that was blocked.
San Marino again found themselves on the back foot after 14 minutes when George McCartney scampered down the left.
He delivered a good cross into the box but the goalkeeper anticipated the situation well and made a comfortable save with Lafferty waiting to pounce on any mistake.
Healy then had his first chance of the match two minutes later but sent his effort wide of the post after being set up by Gillespie.
Davis got into a good position after 26 minutes, only to send his effort straight into the goalkeeper's arms.
The province got their reward for their hard work in the 30th minute when Healy made the breakthrough after a marauding run by McCartney.
He picked out McCann, who in turn squared the ball to Healy. The Sunderland striker reacted quickly and got a touch of luck, his effort taking a couple of deflections before the ball nestled in the net.
It was Healy's 35th goal in 69 appearances and the timing could not have been more welcome.
McCartney almost added a second in the 35th minute but his effort was blocked during a good spell of pressure by the province.
Then Gillespie hooked a shot over the top as they looked to build on their slim advantage.
McCann did just that in the 42nd minute, expertly drilling his effort home from the edge of area after being set up by Healy.
Northern Ireland were intent on improving their goal ratio and McAuley got clear at the back post in the 48th minute.
However, the Ipswich full-back was slightly off-balance and his header drifted wide.
McCann then whipped a delightful ball into the penalty area after 53 minutes but there was no one on hand to take advantage.
Healy, who has not played much at Sunderland, was looking sharper as the game progressed. He turned quickly a minute later only to see his effort taken quickly by the goalkeeper.
Lafferty made it 3-0 in 56th minute following a blunder by the goalkeeper, who pushed a weak shot from Healy into the path of the Rangers striker. He gratefully accepted the gift.
San Marino's troubles increased in the 63rd minute when they were reduced to 10 men with Mauro Marani sent off for lashing out at O'Connor.
Healy almost added a fourth in the 57th minute only for the goalkeeper to clear with his feet.
Rangers midfielder Davis made it 4-0 in the 75th minute with a cool finish following good work from Lafferty.
Substitute Martin Paterson found the net in stoppage time but his effort was disallowed for an infringement.