I just had the same problem (again) and finally came up with the following command macro that takes care of the shell's piping symbol, even in more difficult situations as below

macro cmd_cmd(expr)
    pipemask = "--__|__--"
    @show expr
    expr = replace(expr, "\\r" => "\r", "\\n" => "\n", "\\t" => "\t", "'|'" => pipemask, "\"|\"" => pipemask)
    ex = Base.shell_parse(expr)[1]
    inds = findall(==(:(("|",))), ex.args)
    push!(pushfirst!(inds, 0), length(ex.args) + 1)
    exprs = []
    for i in 1:length(inds) - 1
        args = replace(ex.args[inds[i]+1:inds[i+1]-1], :(($pipemask,)) => :(("|",)))
        x = Expr(:call, :(Base.cmd_gen), Expr(:tuple, args...))
        push!(exprs, x)
    end
    Expr(:call, :pipeline, exprs...)
end

read(cmd`echo 'hello\nhello | world\nhello world' | grep '|'`, String)
# "hello | world\n"