Unfortunately I don't think it will work, you can use an EL3e or 3a in a camera that originally came with an EL3, but not the other way round.
If you compare the batteries one has three electronic contacts, the other only two. The third contact is for the battery meter in your D90, if the camera can't connect to this (because in the case of the older one it isn't there) it won't recognise the battery, sorry.