The 24-year-old Scotland international, who left Town in August 2012 for a club record £8million, helped end Rovers' three-match losing run with a 4-2 victory at the John Smith's Stadium.
Rhodes wore the captain's armband and left with the match ball after shattering a lean spell of just one goal in 11 matches.
Bowyer praised the Scotland international, saying: "It was an outstanding display of finishing and he has been doing it for a number of years now.
"It was special for him coming back to his old club with all his family and friends here. His finishing was different class."
Rhodes' hat-trick made it 20 goals for the season and ended a run of three straight defeats.
Rovers were booed off after home defeats against Burnley and Bournemouth and Bowyer praised his side for their response.
"We have had a sticky patch and the character and spirit of the players was challenged coming into this game but we have responded well," he said.
Blackburn lost Jason Lowe and Rudy Gestede through injury during the first half and had to adjust.
Gestede, knocked unconscious after a clash with Peter Clarke, was stretchered off and taken to hospital wearing a neck brace.
Bowyer said: "We lost two players with injuries and had to dig deep. We have dealt with some criticism from our own supporters this week and come through with flying colours."
Bowyer praised the prompt action of the fourth official who alerted referee Mick Russell to the stricken Gestede and said: "We want to thank him. Rudy has gone to hospital and we hope he will be okay."
Rhodes put Blackburn ahead in the 4th minute when he stepped past Murray Wallace and fired into the bottom corner. Adam Hammill levelled midway through the second half when his cross-cum-shot curled in at the back post.
At the start of the second half Danny Ward missed a great chance for Huddersfield before Rhodes restored the lead, heading in off the post from Craig Conway's cross.
Conway cashed in on a horrible blunder by keeper Alex Smithies who palmed the 25-yard drive into his own net, again off the post.
Nahki Wells ended his own goal drought with his first in 10 matches in the 71st minute to give Town hope at 3-2 but Adam Clayton was caught in possession and Rhodes completed his treble firing past Smithies again.
Town boss Mark Robins refused to blame Smithies or Clayton, but said: "We have gifted them the goals."
"Jordan Rhodes has been on a lean spell but we seem to have forgotten he is no longer a team-mate.
"I am not being derisory to him because he is a great finisher but we have given him the goals."
Robins said it was the "same old story" from his side and warned that his players had to guard against complacency.
"Everybody is saying we are safe but we have to keep on playing and make sure we don't slip up," he said.
"We talk about wanting to get to the next level but we have to consolidate our position.
"I need performances to show me how much work I need to do in the summer and after today's game it looks like a lot.
"We don't have a blame culture and rather than blame individuals we have to learn from our mistakes but it's a difficult one to take."