Quicker? Not in the long run as it turns out :-)

Anyway, if the order is different my original code will not work. Try this instead.

use strict;
use warnings;

use Data::Dumper;

open my $firstFH, q{<}, \ <<END1 or die qq{open: < HEREDOC: $!\n};
DISTINGUERE TRA;1;14;507;0,000000242475382686773;0,0000033946553576148
+2;0,000122935019022194;0,00000000041732202096217;9,18246152003019;9,1
+8246152003019
MANCANTE DI;1;56;507;0,000000242475382686773;0,0000135786214304593;0,0
+00122935019022194;0,00000000166928808384868;7,18246152003019;7,182461
+52003019
APPLICARE SU;1;64;507;0,000000242475382686773;0,0000155184244919535;0,
+000122935019022194;0,00000000190775781011278;6,9898164420878;6,989816
+4420878
MONTATO IN;1;78;507;0,000000242475382686773;0,0000189130798495683;0,00
+0122935019022194;0,00000000232507983107495;6,70441422322555;6,7044142
+2322555
IMPIEGATO IN;2;180;507;0,000000484950765373545;0,0000436455688836191;0
+,000122935019022194;0,00000000536556884094218;6,49796334575812;12,995
+9266915162
RAGGRUPPARE IN;1;109;507;0,000000242475382686773;0,0000264298167128582
+;0,000122935019022194;0,00000000324915002034832;6,22163211731087;6,22
+163211731087
END1

my $recCt     = 0;
my @arr1      = ();
my %arr1Order = ();
while( <$firstFH> )
{
    chomp;
    my( $col1, $lastVal ) = ( split m{;} )[ 0, -1 ];
    $arr1Order{ $col1 } = $recCt ++;
    push @arr1, $lastVal;
}

close $firstFH or die qq{close: < HEREDOC: $!\n};

open my $secondFH, q{<}, \ <<END2 or die qq{open: < HEREDOC: $!\n};
MONTATO IN;1;78;507;0,000000242475382686773;0,0000189130798495683;0,00
+0122935019022194;0,00000000232507983107495;6,70441422322555;6,7044142
+2322555
APPLICARE SU;1;64;507;0,000000242475382686773;0,0000155184244919535;0,
+000122935019022194;0,00000000190775781011278;6,9898164420878;6,989816
+4420878
IMPIEGATO IN;2;180;507;0,000000484950765373545;0,0000436455688836191;0
+,000122935019022194;0,00000000536556884094218;6,49796334575812;12,995
+9266915162
DISTINGUERE TRA;1;14;507;0,000000242475382686773;0,0000033946553576148
+2;0,000122935019022194;0,00000000041732202096217;9,18246152003019;9,1
+8246152003019
END2

my @arr2 = ( 0 ) x scalar @arr1;
while( <$secondFH> )
{
    chomp;
    my( $col1, $lastVal ) = ( split m{;} )[ 0, -1 ];
    $arr2[ $arr1Order{ $col1 } ] = $lastVal;
}

close $secondFH or die qq{close: < HEREDOC: $!\n};

print Data::Dumper->Dumpxs(
   [ \ @arr1, \ @arr2 ],
   [ qw{ *arr1 *arr2 } ]
   );

print
   q{[} .
   join( q{; }, @arr1 ) .
   qq{]\n[} .
   join( q{; }, @arr2 ) .
   qq{]\n};
[download]

The output is the same.

@arr1 = (
          '9,18246152003019',
          '7,18246152003019',
          '6,9898164420878',
          '6,70441422322555',
          '12,9959266915162',
          '6,22163211731087'
        );
@arr2 = (
          '9,18246152003019',
          0,
          '6,9898164420878',
          '6,70441422322555',
          '12,9959266915162',
          0
        );
[9,18246152003019; 7,18246152003019; 6,9898164420878; 6,70441422322555
+; 12,9959266915162; 6,22163211731087]
[9,18246152003019; 0; 6,9898164420878; 6,70441422322555; 12,9959266915
+162; 0]
[download]

Cheers,

JohnGG