Nadal was leading 7-6, 2-2 when rain first stopped play but upon resumption, they managed to go on for another 35 minutes before another shower burst halted proceedings with Gonzalez serving at 2-3 down in the second-set tiebreak.
The first interruption lasted for 75 minutes in what was the first rain stoppage of the championships after 10 days of dry weather.
World number three Nadal and the 11th-seeded Chilean were kept on court for a few minutes before leaving Arthur Ashe Stadium for the locker room, just as they did in the first suspension of play in the last quarter-final match.
Nadal, who has been troubled by an abdominal strain, had gotten a rub down from a tournament trainer before both players left for the locker room at the first break of the action.
The winner of the match will face Argentine sixth seed Juan Martin del Potro.
Top-seeded champion Roger Federer will face Novak Djokovic in the other semi-final scheduled for Saturday.
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