Jenna Westaway from the University of Calgary took the women's track event, while Sherbrooke's Olivier Huet took the men's field award.
Blouin, who finished 19th in pole vault at the London Olympics, claimed the RSEQ conference title two weeks ago with a vault of 4.35 metres. Earlier in the season she set an RSEQ and Quebec provincial record of 4.35 metres at a meet in Montreal.
"Melanie continues to progress very nicely," said Laval head coach Felix-Antoine Lapointe. "Her experience at the Olympics has helped her take her talent to the next level. We're confident she'll take gold once again at the CIS championships."
The other nominees were Elizabeth MacDonald of Dalhousie, Caroline Ehrhardt of Western and Rachel Machin of Calgary.
Philibert-Thiboutot set an RSEQ record in the men's 1,500 at a meet in Montreal this weekend in a time of three minutes 45.71 seconds. At the Golden Bear Open in Edmonton he had claimed gold in the 1,000 metres in a time of 2:24.94, the seventh-fastest time in the country this season.
An injury will keep him out of this week's CIS track and field championships.
"Charles had a great start to the season, especially on 1,000 and 1,500 metres," Lapointe said. "His season-ending injury was very unfortunate but we're confident he will fully recover and will continue to progress in the future."
The other nominees were Connor McGuire of St. Francis Xavier, Anthony Romaniw of Guelph and Calum Innes of Trinity Western.
Westaway had a standout rookie season. In her first appearance at the Canada West championships, she won the 600 metres in 1:30.00 and claimed silver in the 1,000 metres in 2:51.64.
Overall this season, she won four 600-metre finals, two 1,000-metre events and added a victory in the 800 metres.
"Jenna is an outstanding young woman both on and off the track," said Calgary coach Doug Lamont. "She is a great addition to the Dinos’ track and field program and the University of Calgary. Her future is bright."
Alexa-Maude Mallais of Moncton, Laurence Beaudet of Montreal and Andrea Seccafien of Guelph were also considered.
Huet remained undefeated in university meets in his rookie season and went on to capture gold at the Quebec conference championships in the pentathlon (3,644 points) and triple jump (15.46 metres) to help the Vert et Or men claim the team banner.
"Olivier is a complete athlete who brings a lot to our team. He greatly contributed to our return atop the RSEQ men's standings," said Sherbrooke coach Richard Crevier. "He developed on the renowned CREPS circuit in France so he is very sound technically, in many events."
The other nominees were Simon Watts of Dalhousie, Taylor Stewart of Western and Lex Ewen of Regina.
Middle-distance runner Emma Galbraith of Ottawa won the women's rookie of the year award, while 1,000-metre leader Yves Sikubwabo of Guelph won the men's rookie award.
The three-day CIS championships run Thursday to Saturday.