Luke Guttridge and Fraser Franks dropped to the bench with Scott Griffiths missing out altogether, while Alex Lacey, Paul Connolly and Jake Howells came back into the side.
Midfielder Matt Robinson made his 50th appearance for Hatters, while hosts Accrington included new loan goalkeeper Joe Lumley from QPR on the bench.
Stanley: Jay Lynch, Adam Buxton, Luke Joyce, Tom Aldred, James Gray, Kai Naismith, Piero Mingoia, Nicky Hunt, Rob Atkinson, Jordan Mustoe, George Bowerman.
Subs: Joe Lumley, Dean Winnard, Shay McCartan, Josh Windass, Will Hatfield, Marcus Carver, James Alabi.
Jones could loan out Muskwe and Mendes Gomes as he admits certain players would have left regardless of cup exit
Jones still keen on pushing for defensive signing ahead of deadline day
Former Aston Villa and Crystal Palace youngster Williams elated to make his full Hatters debut in Carabao Cup
Luton boss will make a late decision in the transfer window on whether to loan out Pereira
HATTERS RATED: Luton Town 2 Newport County 3
Hatters: Mark Tyler, Paul Connolly, Jake Howells, Steve McNulty, Luke Wilkinson, Alex Lacey, Andy Drury, Matt Robinson, Luke Rooney, Mark Cullen, Paul Benson.
Subs: Fraser Franks, Alex Wall, Elliot Justham, Pelly Ruddock Mpanzu, Ross Lafayette, Luke Guttridge, Jim Stevenson.