Almost a year to the day since Rodgers suffered a catastrophic Achilles tendon injury just four snaps into his debut for the Jets, the fit-again veteran quarterback was powerless to prevent the 49ers from cruising to victory at Levi's Stadium.
The 40-year-old threw for 167 yards with one touchdown and one interception against last year's losing Super Bowl finalists.
Despite the defeat, Rodgers was simply happy to be back on the field after last year's injury that left many wondering whether he would ever play again.
"It felt great," Rodgers said afterwards. "A lot of gratitude just to be back in pads. So many people helped me get to this spot.
"I'm really thankful for my surgeon, my loved ones, my friends, the staff and the training staff to help me get back. Obviously I wanted to take a shot and feel the physicality of it.
"Once I threw a couple balls and took a shot, it felt good."
Although New York took an early 7-3 first-quarter lead with a close-range rushing touchdown from Breece Hall, San Francisco asserted their superiority thereafter.
A 51-yard Jake Moody field goal cut the Jets lead to one point at 7-6, before San Francisco forced a New York punt on their next possession after the visitors failed to advance a yard.
Niners quarterback Brock Purdy then marched his team downfield on a 12-play, 67-yard drive that culminated with Deebo Samuel rushing over from two yards to make it 13-7 after Moody's extra point.
San Francisco's defence then forced another New York punt before Moody's third field goal of the game left the Niners 16-7 up at half-time.
The 49ers kept the scoreboard ticking over in the second half, adding a touchdown through Jordan Mason to make it 23-7 with the first drive of the third quarter.
Rodgers' attempts to generate any New York offensive momentum continued to falter however, with the quarterback tossing an interception on the next drive.
San Francisco took over and Moody duly slotted a field goal to stretch the 49ers' lead to 26-7.
Rodgers showed a flash of his old self after connecting with Allen Lazard for a 36-yard touchdown to make it 26-13 at the end of the third quarter.
But Moody's unerring boot once again ensured the 49ers kept a comfortable advantage, with two fourth-quarter field goals making it 32-13 to the hosts.
With the game lost, Rodgers was removed from the final moments of the fourth quarter, allowing back-up quarterback Tyrod Taylor to throw a consolation touchdown with 25 seconds remaining that made it 32-19.