Trump started the session 10-6 down and already in trouble, with Wilson needing just three frames to wrap up a shock win.
A break of 72 without response from Trump pulled one frame back and gave the 2019 world champion hope, but a crushing 94 break from Wilson took him two frames from a famous win in the quarter-finals.
Trump, who had struggled for form in much of the early stages of the 2020 edition in strange circumstances at the Crucible, hit the first century from either player in the match to reduce the deficit, and then closed out the next frame 70-0.
Wilson then put Trump on the back foot at 9-11 down when he took a 48-0 lead. Trump was unable to take a chance when it was offered to him, allowing Wilson to move into an unassailable advantage in the frame and to within one frame of victory.
Trump had an in in the final frame but a missed long red brought Wilson back to the table, with Trump watching on helpless as his reign as world champion ended as his opponent brought up his first century break of the match. Wilson has now won eight of the 13 meetings between the two men.
The defeat robs Trump of what he had hoped would be a crowning achievement. He had won a record six ranking titles this season but to have become the first ever first-time Crucible world champion to defend his title would arguably have been an even more remarkable success.
Speaking after the match, Trump was stoic in defeat saying: “I’m not disappointed. I battled until the end. Bits of luck that you need to win the tournament weren’t going my way.
“Kyren played some really good stuff. His long potting was amazing, scored pretty heavily and got the run at the right time which is a dangerous combination.
“Minor things can affect snooker in such small ways. The difference between 9-7 and 10-6 is huge.
“If Kyren plays like that and gets a good run of the ball, he will be very tough to stop. His long potting was brilliant. It looks like he has improved.
“He’d definitely be my favourite to win the title."
Kyren Wilson knocks in century to eliminate defending champion Judd Trump
Trump explained that he and Wilson, who were known to rub each other the wrong way, had put their disagreements to bed and was full of praise for his rival.
“We didn’t use to get on that well, but we’ve done a few exhibitions together and get on well now.
“He looks like he has really improved. He’s taken a step up.
"For me, it is all about putting my foot on the gas for next season."
Kyren Wilson knocks in century during dominant evening session