Nadal, the 2008 champion who is seeded No 2 behind Roger Federer, won all 20 points on his serve in the final set and improved to 13-3 in five-set matches.
On the women's side, top-seeded Serena Williams advanced to the third round by beating Anna Chakvetadze of Russia 6-0, 6-1 in 48 minutes.
Williams, the defending champion and three-time winner, led 6-0, 5-0 before dropping a game. Other winners included Maria Sharapova, Caroline Wozniacki and Robin Soderling.
But the big names' acheivements were overshdowed by the incredible events on Court 18, where Izner finished with 112 aces, and Mahut, of France, had 103, with both totals eclipsing the sport's previous high of 78.
There were only three service breaks in the match, the last coming on the final point. They combined to hold for 168 games in a row.
"It stinks someone had to lose,'' Isner said. "But to be able to share this day with him was an absolute honor. I wish him nothing but the best, and maybe I'll see him somewhere down the road, and it won't go 70-68."