The 52-year-old Mexican player shot a 3-under 69, rebounding from a bogey on the par-3 17th with a par on the par-5 18th for a 9-under 206 total. He also won twice on the 50-and-over tour in 2013.
"I got a little bit nervous," Toledo said about of his bogey on the 17th when his tee shot went wide right. "I had no idea where I was in the tournament at the time and I just hit a bad shot."
Watson was trying to break Mike Fetchick's record as the oldest winner in tour history. Fetchick won the 1985 Hilton Head Seniors Invitational on his 63rd birthday.
Watson finished with a 67 after a second-round 65. The Hall of Famer moved into a tie for the lead at 9 under on the par-4 16th with his seventh birdie of the round, but bogeyed the 17th after hitting his tee shot into a bunker and missing a 10-foot par putt. He parred the 18th.
"It was great to be in position to win," said Watson, winless since the 2011 Senior PGA Championship. "I thought I was going to shoot my age again. That was really cool to break my age yesterday, especially here at Pebble Beach."
After opening with a 75 at Poppy Hills, Watson had a 65 on Saturday at Pebble Beach. He won the 1982 U.S. Open at Pebble Beach and took the PGA Tour's Bing Crosby event at the course in 1977 and 1978.
"You remember those times and the positive shots you hit," Watson said. "That's how I played today. I got off to a really good start with four birdies in a row."
Toledo shot a 66 at Pebble Beach in the second round and had only two bogeys in the tournament.
"I finished second to Colin Montgomerie at the Senior PGA this year and I learned a lot," Toledo said. "I learned I had to be more aggressive and make putts and I did."