Use a non-greedy match (same as a greedy match, but with "?" after it).

use Data::Dumper;

my $string = 'WhateverFooBlahBarMoreFooStuffBarMore';
my @words = ( $string =~ /Foo(.*?)Bar/g );
print Dumper \@words;
__END__
$VAR1 = [
          'Blah',
          'Stuff'
        ];
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