The Magpies take on the League One outfit at St. James' Park following a 1-1 draw at the Crown Oil Arena, with the winner of the tie hosting Oxford United in round four.
This will be the Oxfordshire-born official's second game involving the Magpies this term after taking charge of their 1-1 draw at home to Watford back in August. Scott dished out five yellow cards that day, booking United's Paul Dummett and Isaac Hayden.
The 51-year-old was the man in the middle for two of United's Premier League fixtures in 2018/19 - a 4-0 defeat at Liverpool on Boxing Day and a 1-1 draw against Wolves in February in which he booked Jamaal Lascelles, Fabian Schär and Matt Ritchie at Molineux.
Scott, who was promoted to the Select Group of Referees in 2015, has refereed 16 games so far this season, showing 53 yellow cards along with four reds in total.
On Tuesday, he will be assisted by Richard West and Scott Ledger, while Robert Jones will be the fourth official. VAR will be operated by Peter Bankes, with Stephen Child as the additional VAR.