Here's one simple way.

use threads; use threads::shared;

my @file1 : shared;
my $t1 = async{
    my $getfile1 = qq/getS1config.pl/;
    open (FILE1, "$getfile1 |" );
    @file1 = <FILE1>;
};

my @file2 : shared;
my $t2 = async{
    my $getfile2 = qq/getS2config.pl/;
    open (FILE2, "$getfile2|" );
    @file2 = <FILE2>;
};

my @file3 : shared;
my $t3 = async{
    my $getfile3 = qq/getS3config.pl/;
    open (FILE3, "$getfile3 |" );
    @file3 = <FILE3>;
};

$_->join for $t1, $t2, $t3;

## Do stuff with the arrays.
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Note that assigning single scalars into arrays in order to interpolate those scalars into strings is a very dubious practice. You should also be checking your opens and much else. You will have to use lexical variables to use :share

This is a minimal demonstration that could be much improved.