use next inside your loop to skip the blanks. next will skip the current iteration and move on to the next for any loop structure.

while (defined ($rows = <VER>)) {  
    chomp($rows);
    next if ($rows eq '');   # this'll skip blank lines 
    ($rows1,$rows2)=split(/\ /,$rows);  
    $names[$l]=$rows1;
    $versions[$l]=$rows2;
}
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