Argentine manager Gonzalez was appointed last month, but due to visa delays only took his first training sessions this week.
Cruz Azul had the game’s first big chance, Jose Paradela’s shot saved at the near post by Miami goalkeeper Dayne St Clair.
Miami’s opener came in the 24th minute. Though the goalscorer was no surprise, it was a rare Messi header that broke the deadlock.
Luis Suarez crossed from the byline, and the 5-foot-7 Messi outjumped Willer Ditta with a diving header to give Miami the lead.
Suarez nearly turned provider again in the 32nd minute. He received a sumptuous cross-field ball from Messi and scooped it up for German Berterame, whose dinked effort was cleared off the line.
Early in the second half Messi appeared to have scored his 101st Miami goal, racing through one-on-one from a Suarez through ball and placing his shot in off the post, but was ruled offside.
Cruz Azul should have equalized in the 67th minute, but substitute Gabriel Fernandez’s glancing header hit the post, and Casemiro blocked the follow-up shot.