Jones fired into the bottom corner of the net two minutes into stoppage time after second-half goals by Jamie Slabber and Aaron McLean had seen the hosts overturn Jon Challinor's opening strike.
Blues boss Frank Gray was true to his pre-match word and rang the changes for the game with Adam Green, Glenn Poole and Lee Boylan all paying the price for a number of disappointing performances.
Jay Smith, Tom Williamson and Slabber were the men coming in for the home side as Gray tinkered with his system as well as personnel.
Smith's recall after three games out saw Grays switch to three at the back with Williamson coming into the midfield and Slabber up front.
McLean almost ensured the new system got off to the best possible start when he came agonisingly close to scoring after just 12 minutes.
Smith's crafty chip forward was flicked on by Slabber for McLean who unleashed a stunning volley that pinged against the base of the post.
McLean went close again 10 minutes later when he scampered on to a slide-rule pass from Michael Kightly and forced Grecians keeper Martin Rice into a hurried save at his near post, and from the ensuing kick Slabber glanced a header wide.
In what was fast becoming a one-man show, McLean then went close with a couple of stinging long-range efforts
Blues' best chance of the half came six minutes from the break when Rice made a hash of Kightly's corner to allow Djouman Sangare a clear header on goal.
The big Frenchman did everything right but was denied by an athletic clearance off the line by Andy Taylor. The ball then fell at the feet of Jamie Stuart who volleyed into the ground and watched as his strike bounced off the top of the crossbar.
Exeter punished Grays for their profligacy a minute later when Challinor capitalised on some defensive hesitancy to fire crisply past Ashley Bayes into the bottom corner.
The goal was a bolt out of the blue for the visitors who had threatened just once before netting when Taylor's half-volley was comfortably saved by Bayes.
But the goal proved a real shot in the arm and Exeter should have doubled their advantage a minute before the interval when Smith's slip allowed Adam Stansfield a clear run at goal, but Bayes came to his centre-back's rescue and made a brilliant save to deny the ex-Hereford man.
Grays came out for the second half with renewed vigour and got their just rewards seven minutes after the re-start.
Slabber found himself in a yard of space midway inside the Exeter half and made good ground before feeding Andy Sambrook who was overlapping down the right like a steam train.
The ex-Rushden and Diamonds man's delivery matched his enterprising run and there was Slabber to nod into the bottom corner.
Grays continued to turn the screw and Stuart came close to turning deficit into profit when he ghosted in at the back post to meet Kightly's free-kick but Rice was on hand to turn his stab at goal wide.
It wasn't all one-way traffic though and Grecians full-back Danny Woodards tested Bayes with a fierce drive after a mazy run down the right.
But Grays edged in front 11 minutes before the end when Kightly, restored to his favoured right-wing position, got to the byline and squared for McLean who, despite a heavy first touch, fired into the bottom corner.
But the visitors weren't to be denied and, after a sustained spell of late pressure that saw Taylor go close with a rasping free-kick, Jones was on the spot to fire into the bottom corner after being teed up by Lee Phillips.