Morais picked up the problem in training on Monday, with Bantams boss Phil Parkinson admitting he feared the worst when talking about the issue following Tuesday's pre-season friendly at Guiseley.
The confirmation of a ruptured ACL injury for Morais means the Portuguese winger will now be sidelined for anything between six and nine months.
Such an injury unfortunately also means he is now extremely doubtful to play any significant role in the forthcoming 2015/2016 campaign.
Upon hearing the full details of Morais' injury, Parkinson said: "This news is obviously a huge blow for Filipe and sadly confirms our worse fears regarding the injury.
"Fil had stayed back and did all of his rehab early in the summer to recover from his injury last season - I really feel for him.
"We will give Fil all the help and assistance we can, however, to get him back as soon as possible.
"We have to get over this set-back now and continue to make the squad as strong as we can."
Morais is now due for an operation on the injury in the next two to three weeks once the swelling has gone down around his knee.
The player himself took to his official Facebook page to thank the fans for their recent messages.
He said: "I am very sad that I won't be able to help my team-mates on the pitch for some time but I will be there to support them alongside you.
"Thank you all for the messages of support I have received so far. You are all in my heart."