To keep quite on something. To not tell people about something. To not divulge information to people that should not know about something. Keeping certain information limited to a certain group or between two people.
Back in the 60's, passing a joint within view of outsiders got the response: "Keep it low", or "Keep it down low (when you pass it)". This usually happened when riding in a car with friends. Over the years "Down low", "Keep it down low" and "Keep it on the down low" generalized into meaning 'keep it secret' or 'don't be obvious'.
(Old School version):
"Hey, keep it low!"
"Huh?"
"Pass it low!"
"(Puzzled)"
(Laughter from everyone else)
"Keep it down low when you pass it so nobody else can see what you're doing (you dummy)!"
"(Nods head "OK")"