Washington finished second, while Penn, in contention the entire 2,000 meters, was a strong third.
Temple, which didn't qualify for the championship final, took fifth in the consolation final.
Princeton spent nearly three-quarters of the race lurking, never more than a seat or two behind Penn or Washington. With about 700 meters remaining, Khoury called for an all-out sprint, and the surge pushed the Tigers ahead.
Princeton won in a course-record 5 minutes, 29.6 seconds. Washington finished in 5:30.9 and Penn in 5:36.2.
Joining Khoury in Princeton's boat were Martin Crotty, Colin Farmer, Bob Hall, Tim Richter, Morgan Crooks, Ted Carson, Steve Markle and stroke Chris Ahrens.
``This was the fastest race I've been involved in,'' Khoury said. ``We've had some slight disappointments at the IRA the last couple of years, but this turned out to be all I could have asked for.''
Khoury said Princeton is likely to compete next weekend in the national collegiate championships in Cincinnati. He can look forward to another challenge from Penn, which beat Princeton to finish second in the recent Eastern Sprints.
As they returned to the launch area, the Quakers wore grim looks.
``This is kind of disappointing for us,'' Penn senior Hardy Viener said. ``We were second at the Sprints, and we've been going pretty well.
``This was a very long, tough weekend. We had four races in three days, and when we tried to really move, we didn't quite have that zip or freshness. Our conditioning is great, but that's a lot of races.''
Others in Penn's boat were Tom Rymes, Matt Guerrieri, Bill Belden, Jake Watkins, Marcus Dahllof, Gerry Sweeney, Justin Angle and coxswain Hope Varney.
Temple, the perennial Dad Vail champion, stepped up in class and had an up-and-down weekend. The Owls rowed well in the semifinals, but not so well in the petite final. The Owls were timed in 5:50.3, well behind winner Brown's 5:37.0.
``This weekend was a perfect example of our season,'' said freshman coxswain Dennis Anderson, a North Catholic graduate. ``We've been up and down. After Dad Vail, I thought we had a good couple of weeks of practice and had good rhythm. Apparently it wasn't enough.''