Prendergast welcomed a return to competition after their build-up was marred by Williams catching Covid.
She said the pair will be looking to build on the win ahead of the rowing world championships in September at Racice, Czech Republic.
"I think it's just a bit of a sign of how our training has led us to this," Prendergast said of the close finish.
"It's been a different year. For me I've been over in the UK studying and rowing hasn't taken much of a priority as it usually has. And then had a bit of illness leading into this one.
"I think it is really just a sign of our unusual build up to this regatta. We're not too phased by it but know that that will hopefully come with a good solid training block into the world champs."
The women's four of Catherine Layburn, Davina Waddy, Beth Ross and Phoebe Spoors were third in their final.
Matt Macdonald and Tom Mackintosh finished 4th in the men's pair.