Hogan joined Vignette in April 2001 as president and chief operating officer, after serving as senior vice-president of worldwide sales and operations at Siebel Systems.
Vignette also announced the resignation of Joe Marengi from its board of directors. Marengi is Dell's senior vice-president for America, and had been on Vignette's board since July 1999.
Vigenette's chief executive officer change comes two weeks after it warned of lower-than-expected second quarter results, citing "stagnant" IT budgets and spending.
Vignette is due to announce its full results this week, but said it now expects revenue of $34m (£22m) to $35m and a core operating loss of $13m (£8m) to $14m.