Ok, I see progress. Lets get those last warnings out of the way:

First warning you get is for the line where you use substitution. I have an editor with syntax highlighting (emacs in my case, but padre and lots of other editors should have this too) and so could see directly where the problem lies. Look closer at the third substitution, "s/H/Hearts". Do you see it, there is a slash missing?

Quite unrelated, using ',' to string the substitutions together is not working as you probably think it would, but since substitutions work on $_ per default, it actually still does what you want. So you could change the ',' to ';', but it works either way.

Next, you still use @cards[$_] and @newcards[$_] in the string in line 22. Please change that to $cards[$_] and $newcards[$_] or the warning will not go away. Or simply write the line as

print "@cards[0..4],  @newcards[0..4]\n";
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which would have the advantage of printing the 4 cards of each shuffle together.

If you rerun your script now, you get a warning "Global symbol "@cards" requires explicit package name at ./t7.pl line 21". You use @cards on line 21 before you declare it on line 25. And you don't initialize it. Where do you put values into @cards? Since you don't use @random_cards anywhere except in line 16 I suspect you meant to use @cards there. So change the name @random_cards to @cards in line 16 and remove the 'my' in front of @cards in line 25. If all went well you should have the following script, which actually works:

my @startingdeck = ("A H","2 H","3 H","4 H","5 H","6 H","7H","8 H",
                    "9 H","10 H","J H","Q H","K H",
                    "A D","2 D","3 D","4 D","5 D","6 D","7 D","8 D",
                    "9 D","10 D","J D","Q D","K D",
                    "A C","2 C","3 C","4 C","5 C","6 C","7 C","8 C",
                    "9 C","10 C","J C","Q C","K C",
                    "A S","2 S","3 S","4 S","5 S","6 S","7 S","8 S",
                    "9 S","10 S","J S","Q S","K S");
my @cards= @startingdeck;
my $x = 0;



foreach(@cards){
    $_ =~ s/C/Clubs/, s/S/Spades/, s/H/Hearts/, s/D/Diamonds/;
}

@cards = deckof(@cards);
my @newcards = deckof(@cards);
print "@cards[0..4],  @newcards[0..4]\n";
$x++;
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