Woodward attended Mt. San Antonio College before being selected by the Toronto Blue Jays in the 54th round of the 1994 Major League Baseball Draft. He made his major league debut on June 7, 1999, hitting a sacrifice fly in an 8-2 loss to the New York Mets. From 2002 through 2004, Woodward was the starting shortstop in about half of Toronto's games. On August 7, 2002, he achieved a rare feat by hitting three home runs in one game as a shortstop (the first as a Blue Jay and the 15th overall). After an injury-plagued and difficult offensive season in 2004, the Blue Jays released him.