Hi Rolando,

I took this solution from this post:  http://forums.sforce.com/t5/Visualforce-Development/Embedding-Visual-FOrce-page-in-standard-layout-access-to-std/td-p/116543

Basically what you want to do is create a Boolean variable in your controller extension class that indicates whether the master page needs to be reloaded.  An <apex:outputPanel> element can then be used in your inline VF page to refresh the master.  

Controller extension:

public class TestOpportunityControllerExt {
	
	private ApexPages.StandardController controller {get; set;}
	private Opportunity o;
	
	public String pageUrl {set;}
	public Boolean reloadNeeded {get; set;}
	
	public string searchText {
    	get {
    		if (searchText == null) searchText = 'Default Search Text';
    		return searchText;
    	}
    	set;
	}
	
	public TestOpportunityControllerExt(ApexPages.StandardController controller) {
		this.controller = controller;
		this.o = (Opportunity) controller.getRecord();
	}
	
	public PageReference search() {
		reloadNeeded = true;
		return null;
	}
	
	public String getPageUrl() {
		PageReference pr = new ApexPages.StandardController(o).view();
		return pr.getUrl();
	}
	
}

VF page:

<apex:page standardController="Opportunity" extensions="TestOpportunityControllerExt" >
	<apex:form >
		<!--  Do we need to reload the page? -->
		<apex:outputPanel id="reloadPanel" rendered="{!reloadNeeded}" >
		   	<script type="text/javascript">
				// redirect the top level window
				window.top.location.href = '{!pageURL}';
			</script>	
		</apex:outputPanel>
		<apex:pageBlock title="Test Opportunity Inline VF Page">		
			<apex:pageBlockSection >
				<apex:pageBlockSectionItem >

					<apex:outputLabel for="searchText">Keyword</apex:outputLabel>
					<apex:panelGroup >
						<apex:inputText id="searchText" value="{!searchText}"/>
						<apex:commandButton value="Submit" action="{!search}" />
					</apex:panelGroup>
				</apex:pageBlockSectionItem>
			</apex:pageBlockSection>
		</apex:pageBlock>
	</apex:form>
</apex:page>

 Let me know how this works for you as it worked just fine for me in my test.

Regards, Jeremy