Both players are in line for a place in Team GB's Olympics squad.
"Smalling and Jones are young players and, if they don't get a summer's rest, I can definitely see problems," said Ferguson.
"They played in the Under 21 tournament last summer and have not had any real Premier League experience.
"Smalling was playing non-league football two years ago and Jones was in Blackburn Rovers' youth team. So they need a break this summer."