There are 2 potential problems:
1. The intake is sucking in air because the intake joint is above water
Solution: put petroleum jello all around the joint and see if that helps. If it does, use silicon for a permanent solution or get a one piece intake (from Eheim)
2. As others said, the motor is too wimpy to get water over the edge
Solution: fill up the tank and get the flow going and then reduce the water level (your water change in reverse)
Once you get the flow going, having the top of the filter below the desired water level should help to keep the flow going.
One or both should get you going. If not, do post a picture of the intake.
Bump: other, cheap solutions, are to use air pump driven sponge filters or reverse UGF