The third-seeded Isner, ranked 10th in the world, needed only 71 minutes after the two delays to beat 13th-seeded Jurgen Melzer of Austria 6-4, 6-3 in the third round at the Wake Forest Tennis Complex.
The fifth-seeded Roddick, a former world No. 1 player now ranked 21st, fell to 81st-ranked Steve Darcis of Belgium 7-6 (8-6), 7-6 (7-3), in the final hard-court tournament before the U.S. Open next week in New York.
Yet getting on the court proved to be a challenge for Isner and Melzer -- their match was pushed back by a nearly two-hour rain delay, then delayed an additional 45 minutes when it rained again during warmups.
However, Isner didn't show any signs of sluggishness, serving 14 aces -- two coming on second serves -- and breaking Melzer's serve twice in beating the left-hander for the first time in three tries.
"It's never easy playing at night, and the rain made it more difficult," Isner said. "But I played well. I served well, and I hit my second serve especially well. All in all, I'm very happy with the match, and very happy I'm still alive."
Roddick had 13 aces, but the 2003 U.S. Open champion struggled to find consistency with his ground strokes and Darcis' short game, whose drop shots caught Roddick flat-footed several times.
"I did not expect this," Darcis said. "When I came here, I was not playing so good. But I had two good first matches, and here I play very good tennis. ... OK, Andy didn't play his best tennis, but for me it's a great win, especially before the U.S. Open."
Roddick smashed his racket after losing the first set, and argued with chair umpire Carlos Bernardes on a let serve call early in the second set.
"I served Ok, but I didn't return too well and I wasn't hitting the ball clean out there today," said Roddick, who had beaten Darcis in two previous meetings. "If I don't lose serve, I should do fine, and I didn't. That just speaks to how far off the rest of my game was today."
Top-seeded Jo-Wilfried Tsonga of France also advanced to the quarterfinals along with fourth-seeded Alexandr Dolgopolov of the Ukraine, sixth-seeded Marcel Granollers of Spain, and seventh-seeded Sam Querrey.
Tsonga defeated Sergiy Stakhowsky of the Ukraine 7-6 (7-1), 6-4; Dolgopolov beat No. 14 David Nalbandian of Argentina 6-3, 6-4; Granollers rallied to beat Latvia's Ernests Gulbis 4-6, 6-3, 6-2; and Querrey edged ninth-seeded Feliciano Lopez of Spain 6-3, 6-4.