Fly-half Jones, who will join French club Montferrand this summer, kicked 18 points and created a brilliant try for centre Matthew Watkins.
He was the one Scarlets player that Ulster could not handle on a night of raw emotion as Llanelli became Wales's first Celtic title winners.
Ulster played their part in an absorbing championship decider, yet ultimately had to settle for second place behind their hosts, but narrowly ahead of Newport Gwent Dragons.
Jones finished with five penalties and a drop-goal, although it was the magical outside break which created Watkins's try that will long live in the memories of Scarlets supporters.
The visitors were ahead inside four minutes, courtesy of a 50-metre penalty from Humphreys, and it took Llanelli a time to settle.
Jones settled their nerves by stroking over a 14th-minute penalty, yet there was little between the sides during an intense opening quarter.
Humphreys regained the initiative for Ulster through his second successful strike he missed a short-range effort just four minutes earlier.
Jones was at the heart of Llanelli's best moments and a penalty just before half-time edged his team ahead.
Humphreys's second long-range penalty tied things up at half-time, yet Ulster should have been ahead following another uncharacteristic Humphreys miss.
Llanelli had the second half's first scoring chance when Simon Easterby charged down a Humphreys kick. Ulster then infringed during a spell of frantic defending, allowing Jones to complete his penalty hat-trick.
And Jones then showed his ability as an attacker, slicing open Ulster's midfield defence in scintillating fashion to send Watkins over for a try that sent Stradey Park wild.
Jones quickly booted his fourth penalty, while full-back Barry Davies had a try disallowed following a marginal forward pass.
Another Jones strike sealed the deal, offering no way back for Ulster.
: B Davies, Evans, Taylor, Watkins, Finau, S Jones, Phillips, I Thomas, McBryde, Thiel, Cooper, Wyatt, Hodges, Easterby, Quinnell.
Replacements: J Davies, A Gravelle, Griffiths, D Jones, Burn, G Bowen, L Davies.
: Cunningham, S Young, Mallon, Stewart, Topping, Humphreys, Doak, S Best, Sexton, Moore, Mustchin, Frost, Ward, N Best, Wilson.
Replacements: Shields, McCormack, Barker, McMillan, Campbell, Larkin, Wallace.
: Rob Dickson (Scotland).