The 24-year-old Scot, who was beaten 7-6 (7-4) 6-1, had been bidding for a second Grand Slam singles title of the year after his Australian Open victory.
"I lost to the better player. I struggled with my serve and that let him dictate the points," Reid said.
Both Reid and fellow Briton Jordanne Whiley won doubles titles.
Reid and Japan's Shingo Kunieda defended their doubles crown with a 6-3 6-2 victory over Michael Jeremiasz of France and Swede Stefan Olsson.
Whiley won her seventh slam doubles title alongside Kuneida's compatriot Yui Kamiji as they defeated Dutch top seeds Jiske Griffioen and Aniek Van Koot 6-3 4-6 10-6.
Reid led 4-2 in the opening set but Fernandez battled back and went 6-5 up before the Scot forced the tie-break, which he eventually lost.
The Argentine was the stronger in the second set, quickly racing into a 4-0 lead and there was no way back for Reid, who had won his last three matches against Fernandez.
"It's been a good week to get this far, following on from Melbourne," said Reid, who is ranked two places above Fernandez at four in the world.
"Obviously, I wanted a good result but I wasn't good enough in the final.
"He had all the momentum in the second set."
Britain's Gordon Reid lost to Argentina's Gustavo Fernandez in the men's wheelchair singles final at the French Open.