In an enthralling encounter, Tom Cairney opened the scoring with a fine solo goal and though Ivan Ramis equalised, the Championship's player of the month in April, Rudy Gestede, struck a brace to make it 3-1 at half-time.
James McClean pulled a goal back with an emphatic finish but Jordan Rhodes restored Rovers' two-goal lead with his 25th of the season, and despite Nicky Maynard netting a third for Wigan just before the end, Blackburn held on to extend their unbeaten run to 12.
They had a mathematical chance of sneaking into the play-offs before the game but despite falling two points short, Bowyer instead wanted to focus on the strides taken by the club.
He said: "The objective was to win the game. Wigan are in the play-offs and we knew it would be a very good game so our main objective was to win and we did that.
"I thought we played ever so well. We were 3-1 up at half-time and (Wigan goalkeeper Scott) Carson's made a couple of decent saves. The quality of our forward play was exceptional.
"From where we were this time last year when mathematically we still could have got relegated, and the amount of work that's gone in over the summer, we can look on this as progress, but we have to build on that now.
"Our forward play has been very very pleasing and good to watch."
Blackburn's front two of Rhodes and Gestede have scored 38 goals between them this season, despite the latter only joining in January, and Bowyer is excited at what the future holds with those two leading the line.
"The additions that we made in January, Tom Cairney, Gestede, Craig Conway - permanent additions - were outstanding and the confidence that those two (Gestede and Rhodes) have, I'd hate to play against them because which one do you mark?" he said.
"Do you mark the one that's outstanding in the air and can score goals or the one that's a predator and scores 25 goals?"
Wigan manager Uwe Rosler saw his side lose for the third time in four Championship games but felt the only difference between the sides was that Blackburn were more clinical.
Despite this, the German was happy to get the opportunity to freshen up his squad while also allowing long-term absentees such as Ramis, Gary Caldwell and Shaun Maloney to gain match sharpness ahead of the play-offs.
He said: "It was the perfect opportunity for me to give players more match minutes, give players a rest who need it and give players the opportunity to show themselves who weren't starting.
"Obviously we met a team today with a strong end of the season and probably Blackburn are not there where they should be but well done to their manager. They play good staff.
"It was end-to-end football from two very good offensive footballing teams. The difference is they were more clinical than us.
"Second half, our marking in the box and doing simple things right, we have to address that.
"Overall I'm very happy that the team pushed and we look strong. We ended the game by almost equalising.
Rosler's side will meet QPR in next week's play-off semi-final first leg and while he is happy with the preparation, the Wigan manager was keen to remind his side that the tie is over 180 minutes, not just 90.
"We go into next week's preparation in a good mood, with decent momentum," he said.
"I know the way we have played against QPR that we can compete with them. The game will not be won or lost in the first leg and we have to understand that in the way we address it.
"We have to also keep the players who are physically and mentally ready and know what it takes to go further over two legs so that is my challenge to select the right ones (players)."