I agree with Jason that it’d be faster/safer to use an existing Markdown library, but you’re looking for String.prototype.replace (also, use RegExp literals!):
var Text = "[Text Example][1]\n[1][http: //www.example.com]";
var rePattern = /\[(.+?)\]\[([0-9]+)\]/gi;
console.log(Text.replace(rePattern, function(match, text, urlId) {
// return an appropriately-formatted link
return `<a href="https://stackoverflow.com/questions/5835418/${urlId}">${text}</a>`;
}));