Sorry I wasn't more clear. I wasn't suggesting that you change the markup. You can change it in the Page_Load of the page itself.
Let's say you have a style in Main.css that controls the background color of a div in the Master page, with an ID of myDiv.
You can set it to a different color (say, blue) by setting an element-level style on it in the Page_Load of the child page:
protected void Page_Load(object sender, EventArgs e)
{
HtmlGenericControl myDiv = (HtmlGenericControl)Page.Master.FindControl("myDiv");
myDiv.Attributes.CssStyle.Add(HtmlTextWriterStyle.BackgroundColor, "blue");
}