For the second year running, Nadal faces the prospect of playing a string of successive days at the year's last major if he is to win the only grand slam missing from his collection.
Nadal was leading Gonzalez 7-6, 6-6 with the Chilean serving at 2-3 in the tie-break when a second shower burst halted Day 11 proceedings at Arthur Ashe Stadium.
The eventual winner of the last men's quarterfinal will meet Argentine Juan Martin del Potro, who had battled through blustery conditions to beat Croatian 16th seed Marin Cilic 4-6, 6-3, 6-2, 6-1.
Nadal and Gonzalez were to resume their battle no earlier than 1400 (2330 IST) on Friday following the first women's semifinal pitting champion Serena Williams against Kim Clijsters.
The semifinal between Caroline Wozniacki of Denmark and Belgian Yanina Wickmayer will follow the men's contest.
A year after Nadal's semifinal against eventual runner-up Andy Murray spilled into a second day because of the remnants of Tropical Storm Hanna, the Spaniard again ran into foul weather.
Nadal, his groundstroke drives piercing through the swirling winds, lost just one point on his serve until the 11th game when he had to fend off two set points to stretch it into a tiebreaker. After winning the tie-break 7-4, Nadal took timeout to have a trainer treat his strained abdominal muscle before beginning the second set.
They managed to play only four more games when a cold drizzle forced the first interruption of the match.
"In the first set it (the abdominal strain) was very very bad," Nadal's uncle and coach Toni Nadal told reporters.
Seventy-five minutes later they returned to a three-quarter-full stadium where the temperature had considerably dipped and gusting winds swirled through centre court.
Nadal was on the verge of clinching the second set in the 10th game. Gonzalez saved two set points with service winners, but the Spaniard appeared ready to pounce on his third when flying debris caused the umpire to halt play in mid-point.
As Nadal pumped his fist in disgust, the umpire announced to the crowd: "Ladies and gentlemen, will you please make sure you don't leave any napkins or plastic bags around."
The 11th-seeded Chilean saved the replayed set point with a forehand winner and took the second set into another tiebreak.
Seconds later, the players were sent back to the locker room again. After hanging around for nearly two more hours until just after midnight, organisers sent everyone home.
While Nadal and Gonzalez faced an anxious night, Del Potro was already celebrating his second grand slam semifinal of the year. Fighting back after losing the first set and trailing 3-1 in the second, the Argentine induced Cilic into a flood of groundstroke errors and the demoralised Croat lost 17 of the final 20 games.
Cilic had 53 unforced errors in all, compared to just 24 for Del Potro. "My dream is to win this tournament," said the soft-spoken Argentine, who also reached this year's French Open semis.
Results (prefix denotes seeding): Men’s singles quarterfinals: 6-Juan Martin Del Potro (Arg) bt 16-Marin Cilic (Cro) 4-6, 6-3, 6-2, 6-1; 3-Rafael Nadal (Esp) leads 11-Fernando Gonzalez (Chi) 7-6(7-4) 6-6(3-2) - suspended due to rain.
Rain delays play
Steady rain delayed the start of the US Open women’s semifinal between champion Serena Williams and Kim Clijsters on Friday. The men’s doubles final between Leander Paes/Lukas Dlouhy and Mahesh Bhupathi/ Mark Knowles was also hit by the weather.