If anyone getting same issue in version 12. Then this will works for version 12.

I have an alternative solution for this issue.

I created userFunc using COA lib object. And attach f:cObject viewhelper where I need search form of index search in Fluid Template.

<f:cObject typoscriptObjectPath="lib.searchbox"/>

Here is code for userFunc in typoscript.

lib.searchbox = COA
lib.searchbox {
    1000 = USER
    1000 {
        userFunc = TYPO3\CMS\Extbase\Core\Bootstrap->run
        vendorName = TYPO3\CMS
        extensionName = IndexedSearch
        pluginName = Pi2
        controller = Search
        action = search
    }
}

By following configuration Pagination is working fine.