Set the html, body in CSS to have the height of the viewport :
html, body{
height: 100%;
}
Then put the class h-100 also in .row :
<div class="row justify-content-center h-100">
Example:
html, body{
height: 100%;
}
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script><scriptsrc="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js"></script>
<link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css">
<div class="container h-100">
<div class="row justify-content-center h-100">
<div class="col-4 my-auto">
<div class="card">
<div class="card-header">
<div class="row">
<div class="col-2">
<img src="http://s1134.photobucket.com/user/PW_PrimeiroChefe/media/Kratos.png.html"style="height: 30px; width: 30px;" alt="Logo da Empresa">
</div>
<div class="col-10">
<h5 class="card-title">Login</h5>
<h6 class="card-subtitle">nome da empresa</h6>
</div>
</div>
</div>
<div class="card-body">
<form>
<div class="form-group">
<label for="exampleInputEmail1">Usuário</label>
<input type="text" class="form-control" id="exampleInputEmail1" aria-describedby="emailHelp">
</div>
<div class="form-group">
<label for="exampleInputPassword1">Senha</label>
<input type="password" class="form-control" id="exampleInputPassword1">
</div>
<button type="submit" class="btn btn-primary">Entrar</button>
</form>
</div>
</div>
</div>
</div>
