Martial a doubt for FA Cup final - Mourinho
Martial had been expected to feature on the final day of the Premier League season at Old Trafford, but was not even on the bench, with reports claiming he had driven away from the ground before kick-off.
The France international has been linked with a move away from the club, with Juventus, Chelsea and Tottenham mooted as possible destinations.
But Mourinho insisted his absence was purely down to an injury that could also see him miss next Saturday's showpiece.
"He [Martial] is injured. He was injured on Friday, yesterday he couldn't train. He had treatment at the training ground," Mourinho said.
"Romelu [Lukaku] will be back for Tuesday and then we'll have to see about Anthony."
United's victory marked Michael Carrick's final game at Old Trafford, the midfielder setting up the only goal as his lofted pass over the Watford defence enabled Juan Mata to tee up Marcus Rashford.
Jose on @AnthonyMartial: "He was injured on Friday and couldn’t train yesterday. He had treatment in the morning at the training ground and then stayed away. It’s his left knee." #MUFC pic.twitter.com/vEudAHX3Vn
— Manchester United (@ManUtd) May 13, 2018
Carrick will move into Mourinho's backroom team from next season and the Portuguese added: "It was already difficult for me because I got him in the last two years of his career.
"Little problems were coming now and again, so it was a period when he was so, so important but he couldn't have the continuity.
"The moment he's my assistant he will help in every aspect. He has a different vision to everyone else given his experience.
"I will organise my staff in a system where an assistant manager doesn't exist. I will have specific coaches, analysts and no assistant manager. I think it will be Michael Carrick in the future when he has his badges."
Mourinho's long-term assistant Rui Faria is to leave United after the FA Cup final, ending an association that has lasted over 17 years.
Top professional, unbelievable player and all round great bloke. Pleasure playing with you @carras16 pic.twitter.com/er95ma2G1d
— Marcus Rashford (@MarcusRashford) May 13, 2018
Paying tribute to Faria, Mourinho said: "Seventeen years is hard. We spend more time with each other than we do with anyone else in our lives.
"I never had a brother, I had a sister who passed away many years ago. [Faria] is the one who is the closest to a brother."
Watford finished the season 14th in the table on the back of just one win in nine games, but head coach Javi Gracia chose to look for the positives from the campaign.
"I think we arrived at a difficult time for the club. We've done a good job. We had better performances than results," he said.
"I've already spoken many times with the owner. He's ambitious. I don't know what will happen in the future. I'm sure he'll try to improve the level of the squad."