Try doing the inner call from package DB:

eval {
  package DB;
 @ret = &$sub(@args);
};
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There's a few other issues:

• You're making a copy of @_ and passing that copy, but perl passes by reference, and some code uses that (using the &$sub; form of function call fixes this)
• The way you handle $IN_TRACE means you'll never capture inner calls (like if your x() called z()).
• Your inner call is always in list context.

I played with it a bit:

package Devel::TobyLite;

use strict;
use warnings;
use Time::HiRes ();

our $IN_TRACE = 0;

sub DB::DB {}

sub DB::sub {
    goto &$DB::sub if $IN_TRACE;
    my $start;
    my $sub = $DB::sub;
    {
        local $IN_TRACE = 1;

        print STDERR ">> entering $sub\n";
        $start = Time::HiRes::time;
    }
    my (@ret, $ret);
    #package DB {
      if (wantarray) {
        no strict "refs";
        eval { package DB; @ret = &$sub; };
      }
      elsif (defined wantarray) {
        no strict "refs";
        eval { package DB; $ret = &$sub; };
      }
      else {
        no strict "refs";
        eval { package  DB; &$sub; };
      }
    #}
    {
        local $IN_TRACE = 1;
        my $end = Time::HiRes::time();
        print STDERR "<< leaving $sub ", $end - $start, "\n";

        die +(caller), $@, "@_" if $@;
    }
    if (wantarray) {
      @ret;
    }
    else {
      $ret;
    }
}
1;
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Output:

$ ./perl -Ilib -I.. -d:TobyLite -e 'sub x { print qq(ok\n); } sub z { 
+x() } z()' 
>> entering UNIVERSAL::import
<< leaving UNIVERSAL::import 1.40666961669922e-05
>> entering main::z
>> entering main::x
ok
<< leaving main::x 3.29017639160156e-05
<< leaving main::z 8.48770141601562e-05
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