MetadataService.MetadataPort service = new MetadataService.MetadataPort();
service.SessionHeader =  new MetadataService.SessionHeader_element();
service.SessionHeader.sessionId = UserInfo.getSessionId();

MetadataService.Profile profileSystemAdmin = (MetadataService.Profile) service.readMetadata('Profile', new String[]{'Admin'}).getRecords()[0];
for (Integer i = 0; i < profileSystemAdmin.fieldPermissions.size(); i++)
{
    profileSystemAdmin.fieldPermissions[i].editable = true;
    profileSystemAdmin.fieldPermissions[i].readable = true;
}

List<MetadataService.UpsertResult> results = service.upsertMetadata(new MetadataService.Metadata[] {profileSystemAdmin});