The former world No. 5 Gonzalez, who announced prior to the tournament that this would be his final ATP competition, dropped a marathon 7-5, 4-6, 7-6 (7-3) decision to France's Nicolas Mahut on the hardcourts at the Tennis Center at Crandon Park.
Both players managed to save 10-of-14 break chances by their opponent, but Mahut reeled off 12 aces in the match to gain the upper hand.
The 31-year-old Chilean finished with a career record of 371-202 and captured 11 titles.
Argentina's Nalbandian had it slightly easier, earning a 6-4, 7-6 (7-0) straight-set victory over Steve Darcis in just under two hours. Nalbandian saved 5-of-9 break chances by the Belgian to help overcome five double faults in the match.
Also on Wednesday, fading 32-year-old American James Blake succumbed to fellow former top-five star Nikolay Davydenko, 4-6, 6-4, 6-4, promising Bulgarian Grigor Dimitrov whipped Kazakhstan's Mikhail Kukushkin 6-2, 6-2, Czech Lukas Rosol topped Frenchman Michael Llodra 6-4, 7-6 (8-6), Slovak Lukas Lacko drove out American Ryan Sweeting 6-4, 6-4, and Croatian qualifier Antonio Veic overcame American wild card Denis Kudla 2-6, 6-2, 6-1 on Day 1.
Additional opening-round wins came for French qualifier Arnaud Clement, Belgian Xavier Malisse, Dutchman Robin Haase, Croatia's Ivan Dodig, Spanish qualifier Roberto Bautista-Agut, Colombians Alejandro Falla and Santiago Giraldo, and Portuguese Frederico Gil. Giraldo will meet former world No. 1 Rafael Nadal in his next outing, while Falla will face fourth-seeded Andy Murray in the round of 64.
The top seeds for this 12-day event are world No. 1 star Novak Djokovic, former top-ranked greats Nadal and two-time champ Roger Federer, and the 2009 Miami winner Murray. The two-time Sony Ericsson champion Djokovic beat Nadal in last year's marquee Miami finale. Federer is fresh off his Masters championship at Indian Wells.
Nadal and Federer are the all-time leaders with 19 Masters titles apiece.
The winner of this $3.973 million tournament will claim $659,775.