Spaniard Nadal broke service twice in the first set to take it 7-5 and, after the determined and aggressive Gil broke early to go 2-0 up in the second, Nadal took control to close it out 6-3.
Nadal will face the winner of the third-round tie between Russian Igor Andreev and Switzerland's Stanislas Wawrinka.
Nadal's powerful serve was the basis of his victory - he produced five aces and won 76 per cent of points on first service.
Sixth-seeded Argentine Juan Martin del Potro secured his place in the next round with a 6-4 6-1 victory over Serbia's Janko Tipsarevic.
The impressive 20-year-old won 92 per cent of points on his first serve and converted four of five break points for victory.
Another Serb Viktor Troicki dealt with German lucky loser Bjorn Phau 6-4 6-3 to reach the fourth round at Key Biscayne for the second year in a row.
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