Benitez, not unexpectedly, played down the row during his press conference to preview the trip to Teesside, as Sky Sports reported.
Terry has been suffering with a knee injury, but his absence from the team for the defeat at the Etihad Stadium was a surprise. And former Blues striker Tony Cascarino lashed out at the manager for leaving the 32-year-old on the bench in an interview with talkSPORT.
But Terry recently claimed he would be happy to sit on the bench if it benefited the team after a lengthy absence from a knee injury, as the Daily Express reported.
Gary Cahill's illness means Terry is expected to return for the tie at the Riverside Stadium.
With Chelsea's Premier League campaign faltering, the FA Cup takes on a new significance for both the team and Benitez.
The prospect of a trip to Manchester United in the quarterfinals will be a daunting one if Chelsea progress beyond Middlesbrough, but Benitez will be looking for silverware to back up his claims to a leading role beyond this season.
Guus Hiddink did his reputation no harm at all when he guided the Blues to an FA Cup triumph over Everton in 2009 while also ensuring Champions League football the following season after succeeding Luis Felipe Scolari from February until the end of that season.
Sounds familiar, doesn't it? Benitez is in a different position to Hiddink, however. His stock is not as high as the Dutchman's, who was also managing Russia at the same time and enjoyed an outstanding reputation across Europe.
Benitez has been out of work since his dismissal from Inter Milan in December 2010 and could be looking for a new role once his short-term contract at Chelsea comes to an end.
Chelsea have not enjoyed a comfortable ride under Benitez with many supporters still angry at his comments about the club while he was in charge of Liverpool.
Form has remained inconsistent during his tenure, and the Blues slipped to fourth place after Tottenham beat West Ham 3-2 on Monday evening.
Chelsea are now just two points ahead of fifth-placed Arsenal in the race for the fourth spot.
The Europa League represents another chance for Benitez to prove himself on the European stage, but after winning the Champions League last season, UEFA's secondary tournament is scant consolation, especially if not accompanied by access to the elite next year.
Chelsea have sounded out managers such as Manuel Pellegrini of Malaga, according to the Chilean's agent in an interview with El Mercurio, which was reported by The Independent.
If Benitez is not wanted at Chelsea, he has to ensure his name remains high on a list for leading European roles this summer.
One suspects the Spaniard is aware of this and is using his current interim role as the opportunity to impress.
Chelsea have imploded internally on several occasions since Jose Mourinho left the club in 2007.
Scolari told O Globo about his dismissal from Chelsea in an interview reported by The Guardian, and Andre Villas-Boas was deemed to have fallen foul of player power at the club, with Terry, Frank Lampard and Ashley Cole among the senior names at the club as The Sun highlighted a year ago.
In December, Manchester United manager Sir Alex Ferguson told Harvard Business School academics (Daily Telegraph) that constant switching of managers was setting a dangerous precedent for player power.
With Lampard seemingly on his way out at Chelsea, is there another agenda to Benitez's dropping of Terry, whose current contract ends next year, from the team which lined up at the Etihad Stadium on Sunday?
The Chelsea boss might as well go for broke with a ruthless attitude to the high-profile dissenters in the squad if he is to be leaving the club himself in the summer.
The question for Benitez is whether he wants to win at all costs or risk future managerial roles without the talisman that is Terry.