[1,2] is an array reference, not an array. To get an array reference from an array, use  \@arrayname. So in your second case:

while (@rowdata = $sth->fetchrow_array()) {
    push (@chart_data, $rowdata[2]+0);
    push (@chart_labels, $rowdata[0].' '.$rowdata[1].':00');
}
$graph->to_string(\@chart_data, labels=>\@chart_labels);
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