Yes, they could both mean the same thing, but not necessarily. The second one sounds a bit more natural, probably because it clearer. In the second one, it is clear that the total time you spent on your homework was less than 3 minutes. But in the first one, while the most natural interpretation is the same, it leaves the hearer wondering whether this 3 minutes "finishing" the homework was after when you returned from a break after a few hours of working on the homework. Technically, both of them could be used in that context too, but the second one is unlikely to be heard that way.