The 25-year-old striker struck twice in the first half with two impressive headers as Hibs eased past the struggling Staggies at the Global Energy Stadium.
County started brightly and Rocco Quinn and Melvin De Leeuw both had shots deflected behind for corners in the first few minutes.
The visitors’ first effort on goal came in the eighth minute when Malonga dinked past a couple of defenders on the edge of the 18-yard box – but his shot dipped just over.
The visitors took the lead after 22 minutes when Liam Craig found space down the left and whipped in a deep cross which Malonga rose above the Staggies’ defence to head home.
County should have been level a minute later when Joe Cardle sent Yoann Arquin through on goal but the County forward screwed his shot wide of the far post.
Graham Carey sent a dangerous ball into the heart of the Hibs’ box but Jackson Irvine’s glancing header floated wide of the upright.
County continued to press and Arquin missed another great chance when he raced onto a long clearance but dallied too long in front of goal and the chance was lost.
Hibs took advantage of that miss when Lewis Stevenson sent in a cross from the left which Malonga emphatically headed home nine minutes before the break.
The County goal survived an early scare at the start of the second half when a David Gray cross was scooped onto the near post by Jason Cummings.
Arquin came close with a low drive which Hibernian goalkeeper Mark Oxley blocked with his body, as the visitors sat back and let County come at them in the final quarter.
Alan Stubbs’ side were reduced to 10 men eight minutes from time when Dylan McGeouch was red-carded for a mistimed challenge on County winger Joe Cardle by the right touchline.
Referee Stephen Finnie had not hesitation in flashing a red card at the Hibs player – but the visitors held on to book their place in the quarter-finals.