Just to keep track:

my $l;        # all these three variables should probably better decla
+red within the 
my @vals;     # while loop. Only %pairs probably need to be declared b
+efore the while
my $json;

while (<>) {
    $l = $_;
    chomp $l;
    @vals = split /;/, $l;
    if ($vals[0] =~ /Query/) {
        $pairs{$vals[1]}{$vals[2]} = $vals[3];    # %pairs isn't decla
+red anywhere
    } elsif {$vals[0] =~ /Answer/) {              # syntax error: elsi
+f { should be elsif (
        $pairs{$vals[1}{$vals[2]} = $vals[3];
        $json = encode_json $pairs{$vals[1]};     # what do you think 
+is the content of $pairs{$vals[1]}? Probably not what you want to enc
+ode.
        print $json."\n";
        delete $pairs{$vals[1]};
    }
}
[download]

This will still not compile.

Do yourself a favor. Use the following pragmas:

use strict;
use warnings;
[download]