The 40-year-old right-hander became the ninth active pitcher with 2,000. Gibson got his 2,000th strikeout when Pittsburgh's Roberto Clemente was called out on July 13, 1969. Gibson, who died last October, finished with 3,117.
Wainwright had won nine of 10 decisions coming in. The Cardinals trailed 5-0 on a pair of home runs by Tyrone Taylor, but St. Louis rallied to win its 12th straight, 8-5.
Wainwright did not factor into the decision, allowing five runs on four hits in four innings.
Information from The Associated Press was used in this report.