It is a first gold medal for Wiffen, who is from Northern Ireland, since he had surgery on his appendix in August.
It is his second medal of the championships after he finished third behind former Ireland team-mate McMillan in the 400m freestyle final on Tuesday.
“I’m so happy. I went through so many emotions in that race. At the start I was feeling really rough and didn’t know if I could stay at the pace.
“I got to 800m and thought I was done, but somehow I was keeping the gap and I just knew I would have to hammer it in the last 200m.
“That finish shows everything that I’ve been putting in.”
McMillan, from Northern Ireland, added a silver medal to his 400m gold as he came up just short of GB team-mate Scott in the final.
The 25-year-old, who helped Team GB to 4x200m Olympic and World Championship gold alongside Scott, was 0.58 seconds off the lead at the 100m-mark, and although he charged in the closing stages, he had to settle for a silver medal.
Ireland’s Evan Bailey and Poland’s Kamil Sieradzki shared the bronze as they finished 0.94 seconds off Scott’s time of 1:40.54.
Wiffen’s win secured a second gold medal for Ireland in Poland after John Shortt won the 200m backstroke race on Wednesday.
In the women’s 200m breaststroke, Ellie McCartney booked her place in Friday’s final by winning the first semi-final for Ireland.
McCartney set the fastest overall time with 2:18.81, just 0.03 seconds ahead of Great Britain’s Angharad Evans, who won the second semi-final.