Estes carded rounds of 69 and 67 for an eight-under total and will join fellow American Bobby Gates (69, 68) in the second major of the season which takes place at Pebble Beach from June 17-20.
The 44-year-old Estes, a four-times winner on the PGA Tour, will be competing in his 14th U.S. Open. His best finish was a tie for 11th at Pinehurst in 2005.
Thirty-five players competed for the two spots on offer at The Woodlands, one of 13 sectional qualifying tournaments held in the United States this week.
Among those missing out were Australian Steve Elkington and Dallas Cowboys quarterback Tony Romo, who both withdrew after a second weather delay on Monday forced the second round to spill over into Tuesday.
Romo, who shot a 71 in the first round and opened his second round with a quadruple bogey, was unable to return to The Woodlands because of commitments to his NFL team.
"I would have waited it out for sure if I didn't have to be back for practice," the 30-year-old told reporters. "I didn't make it through so that was a negative, but I learned some things that I can use for the next time."
(Writing by Mark Lamport-Stokes in Los Angeles; Editing by Frank Pingue)