The original rule is, if you draw straight line from the 1st to 2nd or 2nd to 3rd base, there is a 3 feet width to either side of that line that the runner have to run within. Based on that rule, Youkilis was not out, because the grass is still inside the 3 feet width of the line.
But there is a new rule, that the runner cannot run 3 feet outsides of the line that he was running. Based on this rule, Youkilis was out because he obviously run more than 3 feet outside of his running line.
There is no rule that says stepped on the grass, and you are out.
The announcers (YES TV) on the English audio channel checked the rule book and explained it.
Also, on the 2nd and 3rd base, if you ran passed the base, the infielder can tag you and get you out. Running pass the base alone does not make an out.