Adam Wainwright picked up a complete game win over Houston today as the Cardinals won 4-3. Not only was Wainwright's complete game unusual because most pitchers don't throw them anymore (it was the 14th one in the majors this season), but Wainwright also batted in the bottom of the ninth inning.
After Brian Barton led off with a walk as a pinch hitter for Jason LaRue, Wainwright stayed in the game and tried to bunt Barton over. After a Brendan Ryan single sent Wainwright to second, Cesar Izturis pinch ran for him. Skip Schumaker singled home Izturis for the win.
The last pitcher I could find who batted in the bottom of the ninth of a complete game win was Greg Maddux. And that was on May 11, 1988. And the game went 10 innings. But Maddux did bat with a runner on base in the bottom of the ninth.
It's quite possible (and highly likely) that another pitcher has batted in the bottom of the ninth of a complete game win, but checking this was pretty tedious work.
UPDATE - On July 2, 1986, Rick Rhoden of the Pirates led off the bottom of the ninth of a 3-3 tie against the Phillies and got a single. Rick Reuschel(!!!) pinch ran for him and eventually scored the winning run.