Boro would have been forced to pay a £1m transfer fee to Portsmouth had O'Neil made his 100th appearance for the club at Home Park, and it is telling that he has not even been named on the substitutes' bench.
The midfielder joined his team-mates on the pre-match stroll onto the pitch, but is not taking part in the warm-up.
He is replaced by loanee Jay O'Shea, who makes his first Boro start after coming off the bench during Saturday's draw with Crystal Palace.
In total, Boro boss Gordon Strachan has made five changes to his weekend team, with Kyle Naughton replacing Andrew Taylor, Julio Arca coming in for Jonathan Franks, and Leroy Lita partnering Lee Miller up front instead of Scott McDonald and Chris Killen, who are both amongst the substitutes.
PLYMOUTH (4-4-2): Stockdale; Duguid, N'Gala, R Johnson, Bhasera; Judge, D Johnson, Clark, Mason; Mackie, Wright-Phillips.
Subs: Larrieu (gk), Fallon, Barker, Eckersley, Folly, Cooper, Bolasie.
MIDDLESBROUGH (4-4-2): Jones; Naughton, Wheater, McManus, Hoyte; O'Shea, Robson, R Williams, Arca; Lita, Miller.
Subs: Coyne (gk), McDonald, Killen, Grounds, Bennett, Franks, Pilatos.