Can I cap off a 2" x 3" downspout?
If you are  not intending to use the downspout for anything but the one purpose than just eliminate the bottom portion all together otherwise you will end up with water just filling up and stagnating in the capped off portion. 

Just divert the downspout with bends, 45 or 90 degree bends, to the to point your are collecting the water so there is not a bottom portion to cap off and collect water.