There must be some other problems, as that's the right syntax to use sqlplus. I tested your stuff, and it worked.

In the same directory, I had those two testing files:

a.pl:

my $rp = system('sqlplus dcs3000/dcua1@AAUA1.WORLD @a.sql');
print $rp;
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a.sql: (Do you have that quit at the end?)

VARIABLE a NUMBER
begin
:a := 0;
end;
/
print a
quit
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From unix shell, I typed:

 
perl -w a.pl
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Everything appears to be fine, and it did run to the end. Quit sqlplus and quit perl.