usando git add -u

git.sh

vquaiato [~/Desktop/foo] (master) $ rm foo 
vquaiato [~/Desktop/foo] (master *) $ git add -u
vquaiato [~/Desktop/foo] (master +) $ git status
# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#	deleted:    foo
#
vquaiato [~/Desktop/foo] (master +) $ git commit -m "removeno foo"
[master 86f025a] removeno foo
 0 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 foo