using pyelftools:

tag = section.get_tag(n)

gives the nth tag of a specific section

The R_X86_64_JUMP_SLOT relocations are applied to the GOT (global offset table) slots, not to the call instructions you're seeing.

The call instructions go to the PLT (Program linkage table) stubs in the .plt section, and those, in turn, use the GOT and the .rela.plt relocations to resolve and jump to the final symbol in the external shared object. This process happens with the help of the dynamic linker (ld.so) and is a little too complicated to explain in this answer box, but you can find more information by searching for these terms.

According to the author @eli-bendersky, pyelftools is a module for parsing and analyzing ELF/DWARF files and it has no direct way of modifying them. I had a look at the module source files and could not find any methods to edit/save either.

On the introductory post, within comments author acknowledges that pyelftools has no API-level support to do this but some tinkering around can help achieve what you need.

If pyelftools is not a hard dependency, here's an example on how to do the same using elffile:

Copyimport elffile

eo = elffile.open(name="/bin/ls")
eo.fileHeader.shnum = 30
with open('./ls.bin', 'wb') as f: f.write(eo.pack())

Using readelf, you can verify that changes were saved correctly:

Copyreadelf -h ls.bin 
ELF Header:
  Magic:   7f 45 4c 46 01 01 01 00 00 00 00 00 00 00 00 00 
  Class:                             ELF32
  Data:                              2's complement, little endian
  Version:                           1 (current)
  OS/ABI:                            UNIX - System V
  ABI Version:                       0
  Type:                              EXEC (Executable file)
  Machine:                           Intel 80386
  Version:                           0x1
  Entry point address:               0x804be34
  Start of program headers:          105068 (bytes into file)
  Start of section headers:          103948 (bytes into file)
  Flags:                             0x0
  Size of this header:               52 (bytes)
  Size of program headers:           32 (bytes)
  Number of program headers:         9
  Size of section headers:           40 (bytes)
  Number of section headers:         30
  Section header string table index: 27
readelf: Error: Unable to read in 0x708 bytes of section headers

There's not much documentation on elffile but you can have a look at the source and figure out ways to replicate pyelftools-specific functionality. If that doesn't work, you can try using both pyelftools for reading/analyzing tasks and elffile to edit sections and write changes.