Damien Duff drove in Johnson's cross early on, but Andraz Kirm soon fired in a deflected equaliser.
Johnson made it 2-1 with a stunning volley and then scored with a lofted finish after Bobby Zamora's flick.
Steve Sidwell lashed in a late fourth as second-placed Fulham secured a win that puts them four points clear of Odense BK and Wisla in Group K.
Johnson showed exceptional technique for his opening goal as he finished first-time on the turn, while the Cottagers turned on the style with their first and third goals, which both came from pretty and intelligent one-touch football, Zamora delivering neat touches in the build-up on each occasion.
The result allowed Fulham to gain revenge for their 1-0 defeat in October's reverse fixture, when they had Moussa Dembele controversially sent off.
It was an ambitious start from both sides and the first chance fell to Fulham as Duff forced an excellent save from Sergei Pareiko with a curling 15-yard effort.
But it did not take the winger long to get on the scoresheet, meeting Johnson's pull-back with a low first-time strike from just inside the 18-yard box.
Wisla quickly levelled after Dickson Etuhu gave possession away, allowing David Biton to surge forward and drill the ball into the Fulham penalty area.
The danger was not cleared and Lukasz Gargula knocked the ball back for Kirm to strike with the assistance of a deflection.
Fulham thought they had restored their lead almost straight away in a breathless first period when Pareiko parried a Duff shot, but Johnson was ruled offside as he knocked in the rebound.
However, Johnson was soon celebrating after he met Danny Murphy's delivery from the right with his superb finish from 15 yards.Continue reading the main story Fulham are unbeaten in 22 home European matches including 17 wins and 5 draws, stretching back to a 0-0 draw against FC Haka on 6 July 2002
Clint Dempsey nearly added a third just before half-time with a determined run and chip over Pareiko, only to see his effort hit the crossbar.
Wisla made a bright start to the second half and Fulham keeper Mark Schwarzer was twice called into action, first saving Gervasio Nunez's deflected 20-yard effort and then smothering Gargula's free-kick.
But Fulham soon had the cushion of a third goal after more outstanding build-up play.
From a well-planned free-kick, Murphy played a diagonal pass to Zamora, close to the penalty spot, and he flicked the ball ahead for Johnson, who dinked it over Pareiko.
The scoring was completed when Sidwell met Duff's cross with a header from six yards out and, although his first effort came back off the bar, he lashed home the rebound.
Kew Jaliens saw a header rebound off a post for the visitors but they were out of the contest - and Pajtim Kasami almost made it 5-1 late on, but Pareiko kept out his close-range header.
Fulham manager Martin Jol: "The second goal was amazing and the third was a clever one. If you could come up with ideas like that every week, you would be like Real Madrid in the golden days.
"You could say we were very efficient because normally we create eight or nine chances and we score one goal and today we were different.
"Johnson for England? If you keep on scoring everyone says you should be in the England team but, for me, as a second striker he is one of the better ones."