Carleton has resurrected its football program this season after pulling the plug on the team after the 1998 season.
Trailing 24-0 in the third quarter, Van Wynsberghe caught a 22-yard pass from Jesse Mills to cut the Waterloo lead.
Carleton had to settle for a field goal and a rouge in last weekend's season-opening 71-4 road loss to the Western Mustangs.
Elsewhere in the CIS it was: No. 1 Laval 20, Sherbrooke 0; No. 3 Queen's 49, Windsor 34; No. 4 Western 58, No. 6 McMaster 15; Ottawa 34, Toronto 10; York 33, Laurier 20; St. FX 31, Mount Allison 10; Saskatchewan 36, Manitoba 34 and UBC 39, Alberta 36 (OT).
At Ottawa, Jamie Cook was 19-of-28 passing for 242 yards and touchdown for Waterloo (1-2). He also rushed nine times for 70 yards and TD
Nick Anapolsky was Cook's top target, hauling in 12 catches for 110 yards and touchdown, Danny Silvestri rushed 13 times for 120 yards and two scores.
Mills finished 11-of-15 passing for 134 yards and the TD to Van Wynsberghe, who finished with six catches for 87 yards.
After Carleton (0-2) finally got on the board, Waterloo exploded with 23 unanswered points in the fourth to put the game well out of reach.
No. 1 Laval 20, Sherbrooke 0
At Sherbrooke, Que., quarterback Tristan Grenon rushed for one touchdown and completed 15 of 28 passes for 167 yards and an interception, but it was enough to power the Rouge et Or (2-0) past the Vert et Or (0-2).
No. 3 Queen's 49, Windsor 34
At Kingston, Ont., the Gaels (3-0) defeated the Lancers (1-2), as quarterback Billy McPhee threw for 297 yards and three touchdowns. Wide receiver Scott Macdonell picked up 97 yards and a touchdown in the victory.
No. 4 Western 58, No. 6 McMaster 15
At Hamilton, quarterback Will Finch threw for 449 yards and five touchdowns while receiver George Johnson had nine receptions for 224 yards and two touchdowns to lead the Mustangs (3-0) to victory over the Marauders (1-2).
Ottawa 34, Toronto 10
At Ottawa, quarterback Aaron Colbon racked up 523 passing yards and three touchdowns as the Gee-Gees (2-1) defeated the Varsity Blues (1-2). Ottawa running back Brendan Gillanders rushed for 102 yards and added 84 receiving yards and two touchdowns.
York 33, Laurier 20
At Toronto, fifth-year starting quarterback Myles Gibbon led the Lions (1-1) to victory over the Golden Hawks (0-3) with three touchdowns. Gibbons finished the game with 211 passing yards and another 155 yards on the ground.
St. FX 31, Mount Allison 10
At Antigonish, N.S., running back Ashton Dickson rushed for 114 yards and two touchdowns as the X-Men (1-0) downed the Mounties (0-1). St. FX quarterback Clay Masikewich had 304 passing yards and a touchdown.
Saskatchewan 36, Manitoba 34
At Winnipeg, quarterback Drew Burko passed for 339 yards and two touchdowns and wide receiver Mitch Stevens had 152 yards and a touchdown as the Huskies (2-0) edged passed the Bisons (1-1).
UBC 39 Alberta 36 (OT)
At Edmonton, Quinn Van Gylswyk kicked a 23-yard field goal in overtime, as the Thunderbirds (1-1) rallied from a 27-point deficit to defeat the Golden Bears (0-2).