while (<>) {
    $l = $_;
    chomp $;                                   # you probably want to 
+chomp $l, or possibly $_ (but you no longer use $_), but not $
    @vals = split /;/, $l;                     # you split your line i
+nto @vals, but no longer use that variable. Besides, 
                                               # declaring @vals with 
+my would be good practice
    if ($l =~ /Query/) {                       # you could use somethi
+ng like: if $vals[0] eq "Query"
        %pairs{$l[1]}{$l[2]} = $l[3];          # where are $l[1], $l[2
+] and $l[3] coming from? Also, %pairs{...} is probably a syntax error
+.
    } elsif {$l =~ /Answer/) {                 # again, you could use:
+ if $vals[0] eq "Answer". Also, "elsif {..." is a syntax error.
        %pairs{$l[1}{$l[2]} = $l[3];           # again, where are $l[1
+], $l[2] and $l[3] coming from? Also a syntax error.
        $json = encode_json $pairs{$l[1]};     # given the previous co
+de, I doubt that you really want to encode $pairs{$l[1]}
        print $json."\n";                      # is you intent to prin
+t to the screen?
        delete $pairs{$l[1]};                  # not sure it's needed,
+ since you just reuse the same variable in the next iteration
    }
}
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With the code you're showing, the hash should not grow significantly, even without the call to delete. (Update:: but this is no longer true with the updated code posted below.)