You were close, but forgot one thing. If you use /ee, you need another set of quotes, and they should be "interpolating" quotes (ie, "...."). Try the following:
use strict;
use warnings;
my $line = "System has tool zigzag version 3.6";
my $match = 'System\s+has\s+tool\s+([0-9a-zA-Z_-]+)\s+version\s+(.*)';
my $replace = '"System has tool $1 version ABC"';
$line =~ s/$match/$replace/eeg;
print "Line after replacement: $line \n";
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Want more info? How to link
or How to display code and escape characters
are good places to start.
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