R. David Murray added the comment:

If the headers are missing, you will get a complaint at the end of the make 
process that it couldn't build the _sqlite module.  It should also have tried 
to import the sqlite3 module and complained if there was an error.  So, 
pre-install, everything looked fine to the build process.

Can you attach your 'make install' log?

(Berker: a key difference in your test is that OP specified an alternate 
--prefix)

----------
nosy: +r.david.murray
resolution: works for me -> 
status: closed -> open
title: import sqlite3 not running -> import sqlite3 not running after configure 
--prefix=/alt/path; make; make install

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<http://bugs.python.org/issue21950>
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