The Scarlets, boosted by the return of five Wales squad members released by Warren Gatland, failed to break their opponents' resolute defence in the 80 minutes and had to settle for four Jones penalties that ultimately wasn't enough.
Coach Nigel Davies made one change from the side that beat Connacht 38-10 in the RaboDirect PRO12 last weekend, with Dominic Day coming into the second row for his 100th appearance for the Welsh region.
The Scarlets camped inside Northampton's territory for the opening ten minutes and Day burst through the line on eight minutes but with defenders clambering around him he failed to ground beyond the whitewash.
Wing Andy Fenby then made another break two minutes later but again the visitors were denied by a last ditch tackle just short of the line.
The Saints weathered the storm and forced their way up the field through a series of scrums which led to prop Waller burrowing his way over the line on 15 minutes.
Fly-half Stephen Myler added the extras before slotting home a penalty moments later for a ten-point advantage.
Opposite number Jones replied with a kick of his own on 23 minutes to bring the sides within one converted try.
With the game being contested fiercely in the midfield there were little opportunities to add to the scoreline before Myler and Jones exchanged penalties to leave the half-time score 13-6 to the Saints.
A few good phases immediately after the interval saw 34-year-old Jones add another three points as Nigel Davies' men began to get a foothold.
But the 2010 LV= Cup winners responded with a well-worked try from Armstrong. Jim Mallinder's side showed patience in and around the Scarlets line before George Pisi fed the winger in the left corner - Myler missing the conversion.
Jones maintained his deadly accuracy with the boot to keep the Welsh region in contention with a long-range penalty but Myler was not to be outdone with his third and fourth of the day to give the hosts a comfortable 24-12 lead.
His replacement on kicking duties, Ryan Lamb, added further gloss to the scoreline with a penalty of his own as Northampton cruised home to secure a date with east Midlands rivals Leicester Tigers in the final next Sunday.
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