Emmanuel-Thomas' goal added to Michael Chopra's strike at the KC Stadium that maintained Cardiff's promotion push.
"He has had a really rough last couple of days," revealed Cardiff boss Jones.
"His grandfather had a stroke so he was really down on Friday and got in late.
"He travelled here with us so that goal would have picked him up a little but.
"And now he is off to see how his granddad is. So full credit to Jay.
"It is nice for him. It's his first goal and his performance the other day was really good and he capped it here with a goal."
The England youth international excelled in Cardiff's 2-0 victory over promotion rivals Leicester on Tuesday and followed it other with another vital contribution in their defeat of the Championship's other form team.
Jones insists Cardiff 'deserved' Hull win
Substitute Emmanuel-Thomas' first Cardiff goal - and his first strike in almost 11 months - was a superb finish from an acute angle, after a show of ball-juggling, in the third minute of injury-time to secure a comprehensive triumph against the Tigers.
Jay Bothroyd had a goal ruled-out for offside while the Cardiff top-scorer also had a penalty appeal turned down after the England international was sent crashing to the ground in the penalty area by Anthony Gerrard.
Hull had been on the joint longest unbeaten run in the Championship and the two goals Cardiff scored against Nigel Pearson's side were just the ninth and 10th goals conceded by Hull at the KC Stadium this season.
"We played some nice football, used the ball well and kept it well," said Jones.
"We had a few cleared off the line, we should have a couple of penalties but we always felt we could score goals."
Third-placed Cardiff maintained their pursuit of the Championship's top two of Queens Park Rangers and Swansea, who also won well on Saturday, with a first win at Hull since 1998.
The Bluebirds are just a point outside the automatic promotion places and need to play just two of the Championship's current top 10 in their 12 remaining league games.
Jones' men play leaders QPR at the Cardiff City Stadium in a potentially crucial meeting on 23 April while the Welsh club finish their season at Burnley on 7 May.
"We're hunting the pack and we want to stay in it," Jones concluded.