Both players had MRI exams on Monday before Philadelphia's game against Miami.
Ruiz has a Grade 2 hamstring strain. He has played in 16 games and is hitting .235 with two RBIs.
"Right now he'll probably be out three to four weeks -- relative time frame," Phillies trainer Scott Sheridan said. "That's kind of what we're thinking right now based on the size of the tear and location."
Howard has had symptoms for the past couple of weeks and is hitting .179 in 16 games this month.
"He's got some changes in his meniscus in his knee and also has some inflammation in his knee that concerns us," Sheridan said. "We did a cortisone injection with him (Sunday) and he's not available to play tonight and we will just treat him day to day right now and go from there."
Howard is batting .245 with six home runs and 22 RBIs in 41 games. He has been replaced at first base by Michael Young.
"If he doesn't respond to the treatment we've provided so far, you've got to re-evaluate what you're doing," Sheridan said. "At no point are we going to put Ryan out there to risk it."