PHOENIX, February 1, 2014 (AFP) - Watson, tied for the lead after a first-round 64, carded a 66 on the par-71 TPC Scottsdale Stadium Course to maintain a share of the lead on 12-under-par 130.
The leading duo were two strokes in front of Australian Greg Chalmers and Harris English, who both posted second-round 67s.
Japan's Hideki Matsuyama also shot 67 to join the group sharing fifth place on nine-under 133. He was tied with Americans Pat Perez (68) and Kevin Stadler (68).
Watson, seeking his first victory since his 2012 Masters triumph, had seven birdies but he bogeyed two of his last three holes -- the seventh and ninth.
Jones, who has a home nearby and is a local favorite, birdied three of the first four holes and after his only bogey of the day at the ninth added another three birdies at 13, 14 and 15 before capping his round with his seventh birdie of the day at the par-four 18th.
Ten players returned Friday morning to complete their opening rounds, and four players failed to complete the second round before it was suspended by darkness.
Along the way players coped with some gusty winds, and Jones was glad to have his second round completed relatively early before the desert temperatures dropped.
"We definitely got the good side of the draw going early," he said. "It's going to be cold and the ball isn't going as far."
Watson was pleased with his round, despite his two late bogeys.
"Everything is clicking right now," he said. "I played really well last week, just didn't make the putts. This time I'm playing well and some of the putts are dropping."
South Korea's Y.E. Yang, who shared the first-round lead with Watson, stumbled to a 73 and fell into a tie for 15th on five-under.
Defending champion Phil Mickelson, who fired a first-round 60 en route to a wire-to-wire triumph here last year, carded a 67 that left him tied for 27th eight shots off the lead.
Mickelson's title defence was in doubt until Wednesday, after he withdrew from the Farmers Insurance Open at Torrey Pines with a bad back last week.
He said his first-round 71 was due to rust rather than any back trouble, and he felt sharper on Friday.
"I didn't make too many sloppy swings," said Mickelson, whose 10 fairways hit in regulation were twice as many as he managed in the first round. "My distance control was back on.
"I don't know if I'm too far back or not, but on this golf course you can really make some fireworks happen."
Leading second-round scores on Friday in the US PGA Tour $6.2 million Phoenix Open (USA unless noted. Par-71):
130 - Matt Jones (AUS) 65-65, Bubba Watson 64-66
132 - Greg Chalmers (AUS) 65-67, Harris English 65-67
133 - Hideki Matsuyama (JPN) 66-67, Pat Perez 65-68, Kevin Stadler 65-68
134 - William McGirt 65-69, Brandt Snedeker 70-64, Patrick Reed 67-67, Scott Piercy 67-67
135 - Morgan Hoffmann 69-66, Martin Laird (SCO) 67-68, Jason Kokrak 66-69
137 - Nick Watney 69-68, Ken Duke 70-67, Kiradech Aphibarnrat (THA) 66-71, Nicolas Colsaerts (BEL) 69-68, James Driscoll 67-70, Hunter Mahan 66-71, Ryan Moore 66-71, Bill Haas 69-68, Jhonattan Vegas (VEN) 71-66, Y.E. Yang (KOR) 64-73, Chris Stroud 70-67
138 - Cameron Tringale 71-67, David Hearn (CAN) 68-70, Chris Kirk 65-73, David Lynn (ENG) 72-66, Ricky Barnes 71-67, Bryce Molder 67-71, Phil Mickelson 71-67, Aaron Baddeley (AUS) 68-70, John Peterson 68-70, Ben Crane 69-69, Matt Every 72-66