How can I use toggle bolts with limited depth behind them?
Are you comfortable with cutting the bolt to a length between 2" and 3"?  That would be simplest.

Another possibility would be to use another piece of wood between your shelf and the wall to create more thickness for the 3" bolts.

If the concrete is actually concrete block, you can drill into that quite easily with a masonry bit from your local hardware store.  If it is an actual poured concrete wall, best not to bother.

ADDED:

To shorten the bolts:

A) Take the bolt to a hardware store, tell someone you want the same bolt but in a 2.5" length - this is likely the easiest thing.

B) Cut the bolts:


Thread a nut onto the bolt and spin it back towards the head.
Use a hacksaw to cut the bolt (if you clamp it, clamp on the nut and head - not the threads) - OR - use a Dremel with a cut-off wheel - OR - use boltcutters!
Unscrew the nut from the bolt; this will clean up the damaged threads where you cut it.