But the young Dragons came flying out of the blocks in the second-half and stormed back with six tries.
Touchdowns from Daniel Thomas and Eli Walker put Wales in front, before the floodgates opened with scores for Darren Harris, Cory Allen, Matthew Morgan and captain Cory Hill.
Wilson was delighted to avenge Wales' shock 38-24 defeat to the south sea islanders in last year's tournament and hopes his side can build on the performance ahead of matches with New Zealand and Samoa.
"It's a very pleasing result especially after last year. We were keen to put things right after that," said Wilson.
"In the first-half we didn't stick to our game plan. We played too much rugby in our own territory and a couple of errors led to turnovers. And as we all know, Fiji are very good at attacking from loose ball.
"But in the second we delivered the game plan to excellent effect. That was the most pleasing thing, the boys showed a lot of maturity to stick to the game plan.
"We really wanted to strangle them up front. Four of our tries came from driving lineouts, two directly and two from the following play.
"We forced a lot of penalties from our scrum and caused them a lot of issues. We were able to get into good field positions and the backs finished well."
Sam Davies, son of former Scarlets coach Nigel, opened the scoring for Wales after just two-minutes of the clash in Stellenbosch.
But Fiji quickly exerted their dominance. Sakiusa Gavidi was wide of the posts on 13 minutes but powerhouse centre Samu Kerevi crashed over a minute later.
Both Matayavusa Lea and Michael Little missed shots at goal to extend Fiji's lead, while Davies also failed to find his range for Wales.
But Josua Kerevi followed up his brother's effort with a score of his own, which Gavidi converted to hand Fiji a nine-point lead at the break.
Whatever Wilson said in the changing rooms at the Danie Craven Stadium did the trick and Wales demonstrated far more commitment and precision in the second-half.
It took just four minutes for Daniel Thomas to haul back in the game. Davies missed the conversion but Ospreys wing Eli Walker, a late replacement for Tom Prydie, who withdrew due to illness, raced clear to hand Wales the lead.
Davies slotted the conversion and extended Wales' lead to 18-13 on 54 minutes.
Replacement hooker Harris continued the onslaught from a rampaging driving lineout on 66-minutes. That begun a five-minute purple patch with Allen and Morgan both crossing with the Ospreys fly-half converting all three efforts.
And the thrilling second-half performance was capped when Cardiff Blues starlet Hill completed the rout at the death.
Wales now face reigning champions New Zealand on Friday but may be without Scarlets centre Owen Williams, who picked up a shoulder injury.
"We thought Fiji were big but New Zealand are just as big and have the skill levels to match," added Wilson.
"But one thing we have in abundance is heart and commitment. As long as we can keep our front-line players on the pitch we can certainly give them a game."