There are more robust ways to do this, but this does what you want.
I changed your filter pattern a bit to make it more robust.
#!/usr/local/bin/perl
use strict;
my $filter = q{user ([^\s]+) has ([^\n\r]+)$};
my $log_string = "user bob has logged on";
$log_string =~ s/$filter/user $1 has accessed the system and is $2/;
print qq{LINE: [$log_string]\n};
Outputs
:!./t2.pl
LINE: [user bob has accessed the system and is logged on]
Wonko
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