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

while (<>) {
    $l = $_;
    chomp $l;
    @vals = split /;/, $l;
    if ($vals[0] =~ /Query/) {
        $pairs{$vals[1]}{$vals[2]} = $vals[3];    # %pairs isn't declared anywhere
    } elsif {$vals[0] =~ /Answer/) {              # syntax error: elsif { 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 encode.
        print $json."\n";
        delete $pairs{$vals[1]};
    }
}