Playing time also is being monitored for third baseman Martin Prado and left fielder Marcell Ozuna.
"When we started the series, we talked with the guys who have been going out there every day for us -- Martin, Marcell," Mattingly said before Saturday's 2-1 loss. "Some of the other guys, we just put a plan together."
The fact Stanton played at all in September was a bonus. The three-time All-Star sustained a Grade 3 left groin strain on Aug. 13, and was reinstated from the disabled list on Sept. 6.
Circumstances are different now that the Marlins are eliminated from National League Wild Card contention.
When Miami still had a mathematical chance, Stanton started against the Mets at Marlins Park. The Marlins also felt an obligation to the Cardinals and Giants, in the Wild Card race with the Mets, to start their regulars.
The Nationals are competing with the Dodgers for the second seed, but Mattingly felt the time was right to rest Stanton, who has 27 homers and 74 RBIs.
"He still wasn't playing at 100 percent," Mattingly said. "Once the games were meaningless, it's harder to take a chance on him having to rehab over the winter. I'd rather him be able to pinch-hit or something.
"The Mets game, we knew we had to. The home field, I can't worry about that too much. Our guys are kind of spent."
Prado, batting .304, did not start on Saturday, but he is expected to be in the lineup in the season finale on Sunday.
Christian Yelich is at 97 RBIs, and he is being given a chance the last two days to pick up three more, which would give him 100 for the first time in his career.
"Yelich wants to play through," Mattingly said. "He's in reach of 100."