for $i ( 0 .. $#Array1) { 
    print "Checking row $i \r";  #only here to prove something is happening 
    for $j ( 0 .. $#Array2) { 
   	if ( $Array1[$i][0] eq $Array2[$i][0] ) 
		{ 
		# Found a match so populate new array.  
		$Array3[$i][0] = $Array1[$i][0]; 
		$Array3[$i][1] = $Array1[$i][1] . ",". $Array2[$i][1] . "," . $j; 
		last; 
		} 
    } #next j 
} # next i

for $i ( 0 .. $#Array1) {  
    print "Checking row $i \r";  #only here to prove something is happening  
    for $j ( 0 .. $#Array2) {  
   	if ( $Array1[$i][0] eq $Array2[$j][0] )  
		{  
		# Found a match so populate new array.   
		$Array3[$i][0] = $Array1[$i][0];  
		$Array3[$i][1] = $Array1[$i][1] . ",". $Array2[$j][1] . "," . $j;  
		last;  
		}  
    } #next j  
} # next i

use strict; 
use warnings; 
use Data::Dumper qw(Dumper); 
my @Array1 = ( 
    [1,'a'], 
    [2,'b'], 
    [3,'c'], 
); 
my @Array2 = ( 
    [7,'x'], 
    [2,'y'], 
    [9,'z'], 
); 
my %hash2; 
for my $j ( 0 .. $#Array2 ) { 
    $hash2{ $Array2[$j][0] } = $j; 
} 
 
my @Array3; 
for my $i ( 0 .. $#Array1 ) { 
    next if !exists $hash2{ $Array1[$i][0] }; 
    # Found a match so populate new array. 
    my $j = $hash2{ $Array1[$i][0] }; 
    $Array3[$i][0] = $Array1[$i][0]; 
    $Array3[$i][1] = $Array1[$i][1] . "," . $Array2[$j][1] . "," . $j; 
} 
print Dumper( \@Array3 );

$VAR1 = [ 
          undef, 
          [ 
            2, 
            'b,y,1' 
          ] 
        ];