Jones took his tally for the season to ten and continued his remarkable sequence of scoring against his old club.
Jones has now scored five in the last four meetings with Sheffield Wednesday, where he spent a productive spell on loan two years ago.
Wednesday did well to equalise the first of Jones' goals but struggled to stay in the match once he had scored again.
The Owls began brightly with Steven MacLean having a goal ruled out for offside after only 75 seconds.
For Southampton, Gareth Bale, who will be staying with the club until the end of the season at least, wasted a scoring chance with a mis-hit shot from 25 yards.
But the Saints were not to be denied and after seven minutes Jones got on the scoresheet for the first time.
Jones seized on a mistake by Wednesday defender Lee Bullen on the edge of his own area to beat Mark Crossley with a low shot from 15 yards.
Wednesday fans in the crowd were reminded by the clinical strike of his spell at Hillsborough, where he scored seven goals in as many matches.
Bullen almost made up for his mistake in the 47th minute with a firm header from a free-kick by Frankie Simek, but Southampton goalkeeper Kelvin Davis smothered the ball on the line diving to his right.
Southampton continued to carve out the best chances and leading scorer Grzegorz Rasiak should have added to his 19 goals in the 49th minute after a shot from Jones had been parried by Crossley.
But under pressure from Bullen, Rasiak could only shoot over the bar from six yards when it looked easier to score.
Wednesday levelled in the 52nd minute when Marcus Tudgay broke free, but lost control after being blocked by the on-rushing Davis. But the rebound fell into the path of MacLean who scored with a low shot from the edge of the area.
Southampton regained the lead in the 57th minute with a classic jump and header by Jones after Chris Baird had picked him out with a centre from the right.
Jones left the pitch to a standing ovation after 72 minutes to be replaced by Bradley Wright-Phillips.
Wright-Phillips almost added a third three minutes later with a shot on the turn which Crossley did well to push to safety.
In the dying seconds Crossley again came to Wednesday's rescue by blocking a shot from the busy Rudi Skacel, as Southampton threatened to build on their lead.