First, replace the Power BI logo with a gif of your choice. It can be included in a div element. This element will encroach on the report's div element. The HTML code is as follows:
<div id="container">
     <div id="overlay">
         <img id="spinner" alt="Alternate Text" src="image/giphy.gif"/>
     </div>
     <div id="embedContainer" style="height: 600px; width: 100%; max-width: 1400px;">
     </div>
 </div> 
Next, make changes in the JavaScript Code. So you final JavaScript embedding code will be:
<script type="text/javascript">
    // Read embed token
    var embedToken = "<% =this.embedToken %>";
    // Read embed URL
    var embedUrl = "<% = this.embedUrl %>";
        // Read report Id
        var reportId = "<% = this.reportId %>";
    // Get models (models contains enums)
    var models = window['powerbi-client'].models;
    // Embed configuration is used to describe what and how to embed
    // This object is used when calling powerbi.embed
    // It can also include settings and options such as filters
    var config = {
        type: 'report',
        tokenType: models.TokenType.Embed,
        accessToken: embedToken,
        embedUrl: embedUrl,
        id: reportId,
        settings: {
            filterPaneEnabled: true,
            navContentPaneEnabled: false
        }
    };
    $("#embedContainer").css("visibility", "hidden");
    // Get a reference to the embedded report HTML element
    var reportContainer = $('#embedContainer')[0];
    // Embed the report within the div element
    var report = powerbi.embed(reportContainer, config);
    report.on("loaded", function (event) {
        $("#overlay").hide();
        $("#embedContainer").css("visibility", "visible");
        report.off("loaded");
    })
</script>
You can also add CSS to align you gif with your report:
<style>
        #container{
            position:absolute;
            width: 1400px;
            height:600px;
        }
        #overlay{
            position:absolute;
            width:inherit;
            height:inherit;
        }
        #spinner{
            display: block;
            margin-top:10%;
            margin-left: auto;
            margin-right: auto;
            width:10%;
            height: 10%;
        }
</style>
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