Your code with one comment:

for(my $i = 0; $i < @filecontents; $i++)
{

    # place each line in file
    # into another array
    # 
    @line = split(/\,/, $filecontents[$i]);
    # XXX           ^------ do you really mean comma?
[download]

In the following, I'll asume the fields are separated by blanks. No need to backslash a comma, BTW.

Ok, what shall we do with @line? assigning to it on each iteration overwrites the previous content.

We need a multidimensional array - a matrix. References (see perlreftut) are handy for that.

    # [] constructs an anonymous array, so we use that.
    # several ways to do it - choose any (not all :-)

    my $anon_array = [];  # gimme an anonymous array and
                          # assign it to $anon_array
    @$anon_array = @line; # assign to the anonymous array 
    push(@matrix, $anon_array);

    # shortcut:
    $anon_array = [ @line ];
    push(@matrix, $anon_array);

    # compacting further: split returns a list, use that
    # to populate an anonymous array on the fly, push that
    # (the SCALAR value which is an array reference) onto
    # the array @matrix
    push(@matrix, [split(/\s+/, $filecontents[$i])]); 
}
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But why do we have all more than one time in memory? (one array holding the lines, another holding the broken-up structure) - back to the file reading.

We can save many a malloc() and brk() and typing just saying

my @matrix;
while (<INPUT>) {
    chomp; # you forgot that - remove trailing newline char
    push(@matrix, [split]);
}
[download]

because while(<INPUT>) assigns to $_, and split by default breaks $_ with the pattern /[ \t]+/, i.e. on one or more whitespace characters.

If you use the <> magic, perl opens each file in @ARGV for you in order, and reads those; using it, your code boils down to

#!/usr/bin/perl

use strict;
my @matrix;

while (<>) {
    chomp; # you forgot that - remove trailing newline char
    push(@matrix, [split]);
}
[download]

If you want to read just one file, you can truncate @ARGV assigning to the array length (well, not quite: the arrays last index):

$#ARGV = 0;  # @ARGV now holds only one element (the first at index 0)
[download]

How do you get your data back? The following prints the value in the 4^th column of the 7^th line (again, see perlreftut):

print $matrix[7]->[4],"\n";
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--shmem

_($_=" "x(1<<5)."?\n".q·/)Oo.  G°\        /
                              /\_¯/(q    /
----------------------------  \__(m.====·.(_("always off the crowd"))."·
");sub _{s./.($e="'Itrs `mnsgdq Gdbj O`qkdq")=~y/"-y/#-z/;$e.e && print}