How to close a file descriptor from another process in unix systems

I don’t know why you are trying to do this, but you should be able to attach to the process using gdb and then call close() on the fd. Example:

In one shell: cat

In another shell:

$pidof cat
7213

$gdb -p 7213

...
lots of output
...

(gdb)

Now you tell gdb to execute close(0):

(gdb) p close(0)

$1 = 0

(gdb) c

Continuing.

Program exited with code 01.
(gdb)

In the first shell I get this output:

cat: -: Bad file descriptor

cat: closing standard input: Bad file descriptor