Since 3.0 I have allowed my PC's to detect a magical invisibility with Detect Magic. Under the rules as written, after three rounds of concentrating, the PC can detect the square containing the invisible creature. Often, they direct their allies to the square. Any attacks still have a 50% miss chance.
This isn't nearly as effective as See Invisibility or the like, and so it isn't used in combat much. Instead it's used to detect clever thieves and the like.
Does this mesh with the Pathfinder rules? I have yet to see anything that says it wouldn't.
It would still work, and is still RAW by the way. Generally I feel if you want to spend three rounds finding out which square to target more power to you. That much (not the right word but I'll go with it) 'wasted' time is going to hurt, as much as using a 2nd level spell when you didn't want to.
Also, if the invisible target of detect magic is mobile, you would have to start over the 3 rnd concentration if it moves out of your area of effect (the 60' cone).
This should work, but only if your target stays in the scanned area for those three rounds.
So yeah, if you can sneak up on an invisible thief picking a lock or disarming a trap or dragging a huge pile of loot with him or something (immobilized by entangle or some other effect should work too), you can detect his invisibility's aura with detect magic.