The legendary coach will now miss the game, having gone into a period of self-isolation.
Boro confirmed the news in a club statement, which read: "The club can confirm that our manager Neil Warnock has returned a positive test for COVID-19 and will be spending a period in isolation in accordance with guidelines.
"Neil is in good spirits and we look forward to welcoming him back after his period in isolation."
Bournemouth responded to the news, saying: "Hoping Neil has a swift recovery and is back on the touchline soon!"
Their upcoming Championship game against the Cherries is one of the EFL's pilot fixtures, meaning 1,000 spectators will be at the Riverside.
Warnock watched Middlesbrough's 2-0 Carabao Cup loss from the stands, with assistants Kevin Blackwell and Ronnie Jepson occupying the dugout.
Jepson also took the media duties after the game, saying: "It was disappointing first half in terms of performance but the work ethic was good.
"Quite a few players were playing together for the first time. It was a good opportunity for our gaffer to see the lads and try and get one or two up to speed.
"Sam Morsy came in, he's only played 70 minutes in the last couple of weeks so it was good to get him in.
"So overall it was positive and I thought second half we grew into it a little bit and got on the front foot.
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"You need something to drop in the box, to come off your knee or whatever.
"In the second half we got a lot in the box but we need to gamble more. But if you put it in the box like we did on Friday night and tonight hopefully things will start dropping.
"The main aim was to give people minutes and give everyone a chance."