To compound Scarlets misery, hooker Rees was sin-binned for a dangerous tackle on replacement Tani Fuga, Malone landing the penalty to reduce the gap to three points.
With Fuga off the pitch and unavailable to throw in at the line-out, Northampton stole a Quins throw and Downey raced clear to give the hosts the lead.
With half-time replacements Tani Fuga, Nick Easter and George Robson thriving the Quins were a rejuvenated side, their pack getting on top as they drove towards the Scarlets line.