Everton will take on West Brom at home in the Premier League on Saturday afternoon.
Goalkeeper Howard recently suffered a knee problem, while defender Stones picked up a hamstring injury.
Both the players could be available for the match against the Baggies at Goodison Park, but Merson had advised Everton manager Roberto Martinez against playing the duo.
“Roberto Martinez cannot bring John Stones and Tim Howard back into his Everton team today,” the former England international wrote in The Daily Star. “The one thing you never do is change a back four and goalkeeper that is not conceding goals.”
“I like Howard, but I think you have to stick with Joel Robles in goal now,” added Merson. “He’s kept three clean sheets and the fans will get restless if Howard plays. Changing a winning team is asking for trouble.”
Howard has kept six clean sheets in 23 Premier League appearances for Everton so far this season, making three saves per game and 2.03 saves per goal on average in the process.
Stones has created three chances in 21 Premier League matches for the Toffees so far this campaign. The 21-year-old England international centre-back has a pass accuracy of 89%, and has won 28 headers, 19 dribbles and 28 tackles.