This requires the latest version of apktool.
apktool d $APK_PATH -o $OUTPUT_FOLDER
# Open the apktool.yml text file
# Alter the versionCode and versionName entries
# now rebuild!
apktool build $OUTPUT_FOLDER
# next you need to re-sign the apk with the original keystore file
jarsigner -verbose -keystore $KEYSTORE_PATH -storepass $KEYSTORE_PASSWORD -keypass $KEYSTORE_KEY_PASSWORD $APK_PATH $KEYSTORE_KEY_NAME
~/android-sdk/build-tools/21.1.1/zipalign -v 4 $APK_PATH $APK_OUT_PATH
@KhumarOzzie
the last two lines are in fact two lines. if you thought they were word wrapped and put them on the same line you get illegal option error.