split is the way to go.

Another option:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $str = q{one="1" two="2" three="3" ... x="y" };
my @list;
while ($str =~ m/(\w+)="([^"]+)"/g){
    push @list, [$1, $2];
}
print Dumper \@list;
[download]

The reason why you can't put them all into $1, $2, $3, ... is that the mapping from parenthesis groups to numbers is done at the compile time of the regex.

Update: fixed small glitch in regex, pc88mxer++ for pointing out.

Second update: There is another way involving just one regex, but it uses the evil and experimental (?{...}) code assertions. Read the warnings in perlre before using it.

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $str = q{one="1" two="2" three="3" ... x="y" };
our @list;
$str =~ m{
    (?>
        (\w+) # key
        =
        "([^"]+)" # value
        \W*       # anything inbetween
        (?{ push @list, [$1, $2] })
    )+
}xs or die "No match";
print Dumper \@list;
[download]