Have you tried the perlipc manpage?

The section headed Safe Pipe Opens (about a third of the way down the page) may provide a solution.

One of the nice things about Perl scripts is that the source is (unless someone has gone out of their way to obscure it) readily available. Rather than struggling with inter process communication, driving an interactive interface and parsing the text messages out of script2, you might think about incorporating the relevant subroutines of script 2 into script 1.

#!/usr/bin/perl
use warnings;
use strict;
use IPC::Open3;
use IO::Select;

my $pid = open3(\*WRITE, \*READ,\*ERROR,"/bin/bash");

my $sel = new IO::Select();

$sel->add(\*READ);
$sel->add(\*ERROR);

my($error,$answer)=('','');

while(1){

 print "Enter command\n";
 chomp(my $query = <STDIN>);
 
 #send query to bash
 print WRITE "$query\n";

 foreach my $h ($sel->can_read)
 {
   my $buf = '';
   if ($h eq \*ERROR)
   {
     sysread(ERROR,$buf,4096);
     if($buf){print "ERROR-> $buf\n"}
   }
   else
   {
     sysread(READ,$buf,4096);
     if($buf){print "$query = $buf\n"}
   }
 }
}

waitpid($pid, 1);
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To capture the output of a script you can use backticks, like this:

my $output = `some_script.pl`;
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This approach won't work. The backticks are blocking the execution and you need to provide the input. So it's a dead-lock. Better to look at perlipc. Though the most generic approach is use of pipes and forks. The "open" command with "-|" or "|-" is very convinient for this. For example

# this makes the fork and pipes STDOUT of child to OUTPUT of parent.
my $pid = open(OUTPUT, "-|");

if($pid == 0)
{
    # we are in child now. To provide input I need another fork.
    # This time the STDIN of child is piped from INPUT of this process
+.
    my $another_pid = open(INPUT, "| another_script_or_program");
    # now check the return value and pass the input thru INPUT
    print INPUT "my input\n";
    exit(0);
}

# the main process just reads data from OUTPUT
print while(<OUTPUT>);

# do waitpid
close(OUTPUT);
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oh yes, you're right. Definitely a case for pipes.

Nothing from CPAN? That is harsh!

You will need to look at perlipc for "open with pipes".