I would expect that Tibbets would have been ordered to auger his plane into the sea rather than allow the bomb to be captured intact, but in the interest of fantasy, let's imagine he doesn't.
Nothing much changes, other than a lot of people in Hiroshima get to go about their lives. As quickly as possible, once it's determined the raid was not completed, the second bomb would be rushed to its target, whether it be Nagasaki, a return to Hiroshima, or some other location.
Given enough time, Japanese scientists would probably be able to make something of it. But unless the Enola Gay landed completely intact (and if it was a crash landing, that's extremely unlikely) they wouldn't necessarily have access to arming mechanisms, etc. to detonate the bomb. The time required just to dig the thing out (it was far heavier than standard bombs) would be considerable. Add more time to figure out just what was so special about it -- assuming they can open it up, etc. Some other city would have long since been in cinders. And while a subsequent, successful bombing would certainly open the eyes of His Imperial Majesty's government as to exactly what they'd captured in Hiroshima, they still would have no reasonable way to deliver it, even if they could jury rig some way to arm it.
And finally, Japan had no idea how many additional bombs the US might possess. That consideration alone would probably forestall any considerable change in Japanese strategy. The war was as good as lost at Hiroshima in OTL; Nagasaki just sealed things.