In the heat, the duo faced Luca Spik and Iztok Cop, of Slovenia - the former Olympic champions - and the race developed into a dog fight between the two crews for direct qualification to the semifinal.
Neck and neck with 500 metres to go Waddell and Cohen made their move and took the lead from the Solvenians, taking an impressive clear water win.
Waddell, 33, who has raced with a heart ailment throughout his career, last competed on the world stage when he won gold in the single sculls at the Sydney Olympics in 2000.
He turned to yachting and was part of Team New Zealand crews at two America's Cups before making a return to rowing.
Waddell challenged triple world champion Mahe Drysdale for NZ's only single sculls place at the Beijing Games but lost out after an epic duel. But the success of the New Zealanders in Lucerne overnight was blighted by the withdrawal of Olympic champions Caroline and Georgina Evers Swindell in the women's double scull.
Rowing New Zealand spokesman Richard Gee said Georgina had showed signs of a cold and team officials decided give the double scullers a break considering their upcoming training schedule. "With a heavy training schedule ahead of them in coming days and weeks, it was decided there was nothing to be gained from racing in a world class field at 95 percent,"
Out on the Rotsee course, New Zealand lightweight single scull world champion Duncan Grant - competing in the non-Olympic class of the single scull - dominated his heat to win by almost six seconds.
Under-23 champion Emma Twigg dominated her heat leading all the way to finish in 7 minutes 38.09 seconds, the sixth fastest qualifiers.
World champion Mahe Drysdale secured his place in the semifinal with a heat win, cruising out behind Switzerland's Andre Vornarburg before moving through at half way and sculling out to a five-second margin at the close.
In the women's coxless pairs, the 2005 world champions Nicky Coles and Juliette Haigh had a tough looking race against the Chinese number two boat and the USA in their heat.
The New Zealanders chased the USA and got themselves ahead of the Chinese at halfway. The USA pair were never more than a length ahead, and Coles and Haigh came through in a strong second place to book their place in the semi-final.
In the men's coxless pair Nathan Twaddle and George Bridgewater - champions in 2005 - lined up against the Chinese number one boat, the Irish, the French and South Africa.
The New Zealanders led at half way and with only first place securing direct qualification to the semi-final, they took control of the race.
Twaddle and Bridgewater finished the race with a commanding one and a half length lead over South Africa.
The New Zealand men's coxless four had a smooth passage to their heat win over Germany and Canada.
New Zealand has yet to qualify boats for Beijing in the men's and women's lightweight double sculls.
Candice Hammond and Louise Ayling battled for fourth behind China, Denmark and Cuba, with another shot in the repechage. Storm Uru and Peter Taylor put a disappointing Munich behind them with a much better row to win their heat.
