I made 2 files: patternfile and testfile, each containing 1 word "perl". The following worked. So I'm guessing your variable filenames are screwed up, or you don't know that the -f option precedes a patternfile, OR you are not getting any matches.

#!/usr/bin/perl
my $ouput = `egrep -f patternfile testfile > output`;
print "$output\n";
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#prints nothing, but output contains the word perl

The following also works

#!/usr/bin/perl
my $p = 'patternfile';
my $t = 'testfile';
my $o = 'output';

my $ouput = `egrep -f $p $t > $o`;
print "$output\n";
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