I think that graff has the basic idea. There are some specific gotchas about isql from the command line that I have come across over the years.

my $qrycmd = '-S[Server] -U[userid] -P[password] -h-1 -n -s:';
# -h-1 suppresses headers
# -n removes numbering and the prompt symbol (>) from input lines
# -s: sets the field seperator to a colon, :, this eliminates a space
#     between fields and in the first position of the line (tabs, \t,
#     doesn't work reliably

open( DB, "isql $qrycmd -iperlmonk34.sql |" ) or die "can't run isql: 
+$!";

while (<DB>) {  # assuming the tool prints one line per row
    chomp; # remove newline
    my ( $lname, $fname ) = split(/:/); 

# the if statement accounts for the last two lines of the isql output
# which consists of a blank line followed by a line listing rows 
# affected
    if(defined $fname){
        push @fnames, $fname;
        push @lnames, $lname;
    }
}
close DB;
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