But right-hander Woody Williams is throwing and hopes to return to the rotation by the end of June after being out since May 12 with a strained left calf muscle.
Dr. Lewis Yocum will perform the surgery on the 33-year-old Estes Wednesday (June 7) in Los Angeles.
Estes had been on the disabled list since April 7 after suffering a strained flexor tendon in his elbow during his first start of the season two days earlier. In the sixth inning of the season's second game, Estes felt a pain in his elbow while throwing across his body after fielding a bunt at Petco Park.
"There were two distinct injuries," said Padres trainer Todd Hutcheson of Estes. "The ligament in the elbow didn't look extremely good in the first (MRI) exam of the elbow."
Estes was rehabbing on schedule until he felt pain in the elbow May 23 on the second curve ball he threw during a bullpen session in San Diego.
After throwing 30 fastballs from the mound, he started throwing curves. On his second curve, Estes felt pain in his elbow. He stopped throwing after the next pitch. A subsequent MRI exam showed the separation in the ligament had increased.
Estes made the decision to have "Tommy John" ligament replacement surgery after consulting with a third physician earlier this week.
"There was a 20 percent chance he could rehab the injury and pitch again this season," said Padres manager Bruce Bochy. "But if he came back, he probably would have had to take the curve out of his repertoire. That's a big pitch for him. We agreed that this was the best thing."
Estes signed a one-year contract with the Padres last winter for $1.1 million. At the time, Estes was rehabbing a stress fracture to his left ankle that limited him to 21 starts last season with Arizona.
"We were concerned about his foot in spring training," said pitching coach Darren Balsley. "We limited his running. He had a solid spring and we were expecting a big year out of him. There were no symptoms of elbow problems in the spring."
Williams, meantime, said he expects to be back in the Padres rotation by the end of the month.
"Everything is going good," said Williams, who suffered the calf strain while running the bases in Chicago. "I have to build up strength in my calf more."
Williams was 3-1 with a 3.27 earned run average when he was injured. The Padres were 6-1 in his seven starts.
REPLAY: San Diego might be the wrong venue for Chan Ho Park if Friday night's game at Pittsburgh is a true indication of what he can do.
Pitching in a steady rain that turned PNC park into a quagmire, Park not only shut out the Pirates on five hits over six innings, he went 3-for-3 at the plate with two RBIs -- matching career highs in both hits and runs batted in -- to lead the Padres to a rain-shortened 7-0 victory.
Mike Piazza and Brian Giles both hit two-run homers for the Padres, and Giles drove in a third run with a single in a game shortened to six innings.
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