The American rolled in five birdies at the Spyglass Hill Golf Course to add a second round 67 to his opening round of 64 to head into the weekend on twelve-under.
It was Snedeker's long game that was particularly impressive, with the world number 63 finding every green in regulation as he made light work of the trickiest of the three courses in use.
Jones went one better than Snedeker, carding a 64 at Spyglass in a round which included eight birdies and two bogeys.
One shot off the pace is Justin Hicks. The overnight co-leader carded a 68 at Monterey Peninsula to go with his opening 64. A group of ten players, including Billy Horschel, find themselves on ten-under.
Jason Day, the winner at last week's Farmers Insurance Open, was one of the big movers of the day, recovering from a mediocre opening 72 to post a scorching 62 on Friday.
The Australian produced eight birdies, one eagle and a lone bogey on 18 as he rose 85 places to sit on nine-under alongside among others Jim Furyk and Nick Watney.
J.B. Holmes, one of the men Day defeated in a play-off at Torrey Pines, had a very different day, with a triple bogey on the 17th – his ninth hole on the day – seeing Holmes slip back to six-under.