Ryan Lamb, who replaced Stephen Myler five minutes from time, rescued a losing bonus point for Saints with a 79th-minute penalty.
Saracens welcomed back captain Steve Borthwick, out for six weeks with a torn calf muscle, and fly-half Hodgson, who missed the Six Nations defeat to Wales with a hand injury.
Tom Wood, out injured since January 6, was on Northampton's bench.
Flanker Wood appeared to be England head coach Stuart Lancaster's original choice to captain the national side during the Six Nations before suffering a fractured big toe.
Myler kicked off low towards what looked close to a waterlogged Saracens 22, and was offered the opportunity to open the scoring six minutes later, but pushed his penalty wide.
Referee David Rose penalised Saracens again three minutes later for pulling down a maul, and this time Myler managed to steer his kick inside the left-hand post.
Hodgson equalised in the 12th minute after Northampton were guilty of tackling Ernst Joubert while he was in the air.
He then gave Sarries the lead in the 16th minute after referee Rose deemed Saints had failed to roll away from a tackle on the edge of their 22.
It required a fine tackle by Duncan Taylor to prevent Scott Armstrong scoring the game's first try for the visitors when he broke up the left wing at pace.
Myler had the chance to level matters after 21 minutes but he repeated his first attempt, failing to make the ball turn inwards, and it sailed beyond the far post.
When Rose called Saracens for going off their feet at a ruck Myler, his confidence seemingly fragile after two misses from three, chose to kick for touch only for Saints to be shunted backwards in a subsequent maul.
He reverted to going for goal when Saracens went offside in the 35th minute - and another shaky effort crept over the bar after striking the inside of the post, bringing the scores level.
But the visitors then conceded a penalty in front of their posts on the stroke of half-time. Saracens went through the phases, waiting for an opponent to test Rose's patience - and Roger Wilson obliged, penalised for not releasing after tackling. Hodgson sent Saracens in at the break 9-6 ahead.
Within eight minutes of the restart Hodgson added his fourth penalty after Saints collapsed a maul. His fifth, in the 52nd minute, was a tremendous long-range shot to punish an offside offence.
Myler reduced the arrears three minutes later when Rose punished Saracens rather harshly for a dubious accidental offside.
Wood then returned to the field in the 57th minute, watched closely by England coach Andy Farrell.
But it was the ruthless Hodgson who widened the gap after 63 minutes, his sixth successful strike from six attempts in a very impressive performance.
The only disappointment was the absence of anything resembling a try-scoring opportunity, but then wretched conditions contributed to handling difficulties for both sides, as did the number of scrums that had to be re-set.
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