In an evenly-fought contest, a moment of quality was always going to settle it and former Tractor Boy Rhodes provided it in the 64th minute when he ran on to Rudy Gestede's cushioned flick to clinically fire into the bottom-right corner from the edge of the area.
Gestede missed from point-blank range but got Blackburn's second with 10 minutes to go, heading in Craig Conway's pinpoint free-kick.
Bowyer spoke highly of Rovers' record signing Rhodes after his 50th league goal for the club.
He said: "I thought it was an outstanding goal. A through-ball from Rudy and he's took it with his left foot and it's a fantastic finish.
"I find it difficult to find more words to say about him other than 'phenomenal' and 'outstanding'.
"We always knew it was going to be very difficult against Ipswich and Mick McCarthy's team. They never stop. A clean sheet and two strikers scoring, it was a very pleasing performance.
"The whole team worked ever so hard and on the back of the game on Tuesday, the effort from everyone was superb. We needed that second goal because Ipswich don't let off.
"That's 13 clean sheets for the season and the effort and energy levels of our lads today was superb."
The win was Blackburn's first at Ewood in over a month and their first victory after four draws, but on the flip side they are enjoying their longest unbeaten league run - six games - and with his side seven points from the top six, Bowyer has not given up on sneaking crashing the end-of-season party.
"We've got to keep going. That takes us to six games unbeaten now and there's six games left so there's a hell of a lot of football left," he said.
"You've seen the results today in the Championship. Things change very quickly."
Ipswich boss Mick McCarthy believes it will be difficult for his side to reach the play-offs after a defeat which leaves the Tractor Boys five points away, but felt there was not much between the teams except the quality finishing of Rhodes.
He said: "I think we were equally as good or equally as bad as the opposition up until that goal went in because it wasn't a great game.
"I actually thought in the second half we were all right. First half, I was quite happy with it and we let them off the hook. We just blinked first.
"But it's an £8million striker's goal, and good touch from Gestede. It was poor defending from us but there's poor defending lots of times in games and it's whether you can punish it and he did.
"He's a very good player at this level. There's no question about that.
"I don't think he'd had a kick up until that, and that's the difference between winning games and not. It wasn't a great chance, he's hit it from 18 yards but the bounce has just beaten Gerks.
"It's always important to bounce back but as games are running out, it's not going to be easy.
"We've got to come back and do it again. Six games to play, see how many points we can get. We're not in the best position to get in the play-offs. Reading are in that and it's theirs to lose now."