The 25-year-old Italian came on as a half-time substitute as the Owls lost 1-0 to Boro in the Championship.
Forestieri had played 72 minutes on Saturday as Wednesday beat Birmingham.
"Fernando came to talk to me and said 'I'm not ready to play 90 minutes because I don't feel energy'," Carvalhal told BBC Radio Sheffield.
"He said 'If you need me during the match I am ready'."
Former Watford player Forestieri scored twice on Boxing Day, helping Wednesday to a 3-1 win over Blues at Hillsborough and taking his personal tally to 10 for the season.
Forestieri's omission at Middlesbrough was one of six changes Carvalhal made to his starting XI for their trip to Teesside.
"We must talk about the conditions that we played this game," said the Portuguese.
"Some of the players played two days ago. We analyse player-by-player and check which are available to play the game.
"Some of them recover better than others. We can't put players at risk."
Carvalhal was frustrated Middlesbrough had a nine-day break between matches, as their game at Blackburn on Boxing Day was postponed.
"I wish to play with my players in the same condition as Middlesbrough," he added. "This makes a big difference. I can't ask any more of my players.
"If it was the other way around I am 90% sure we would win the game."
Sheffield Wednesday forward Fernando Forestieri did not start Monday's game at Middlesbrough because he felt tired, according to boss Carlos Carvalhal.