After rallying from a break down in the deciding set, the world number six will next meet the winner of Alexander Blockx's meeting with Yannick Hanfmann.
"It's tough. Not just (playing against) another American, but probably my best friend out on tour, or one of a few," Shelton said.
"His trajectory has been steep lately, so I'm happy to see the way he has been climbing (the rankings)," Shelton added of the 112th-ranked Nava.
"I know he wasn't feeling 100 percent today, so I feel bad about that. I hope he gets back to 100 percent quickly, because he's playing great on the clay."
The win improves Shelton's perfect record to six wins from six outings in 500-level events this year as the 23-year-old tries to go one better than last year on the Bavarian red dirt in pursuit of a career-first clay-court title.
Shelton lost the 2025 title-decider to Alexander Zverev, and the German is once again the top seed in this edition of the tournament. He will meet Miomir Kecmanovic in his opening match.
The winner of that encounter will face Gabriel Diallo in the round of 16 after the Canadian beat Ukrainian qualifier Vitaliy Sachko 6-1, 6-2.
Elsewhere, Argentinian fifth seed Francisco Cerundolo won 6-2, 6-2 against Sumit Nagal of India, while French seventh seed Arthur Rinderknech eased past the US' Alex Michelsen in straight sets.