Simpson caught one pass for six yards in the Bengals' 13-8 loss.
The organization believes Simpson, who has been active in community charities, should get the benefit of the doubt under the position of "innocent until proven guilty," team and league sources told ESPN senior NFL analyst Chris Mortensen.
Simpson was excused from practice on Thursday and Friday. The team said in a statement that the coaches considered him ready to play. Andre Caldwell was expected to start in his spot.
Simpson took over as a starter this season after the Bengals allowed Terrell Owens to leave and traded Chad Ochocinco to New England. He leads the team's receivers with 180 yards and is tied for second with eight catches.
"Jerome's legal situation with regard to events of the past week remains completely unresolved, and the Bengals believe it is not appropriate to act on any presumption of what may transpire," the statement said.
Police on Wednesday confiscated a package containing 2.5 pounds of marijuana shipped from California to Simpson's house in northern Kentucky.
Bengals tackle Anthony Collins also was present at the house, along with a woman who signed for the package.
Police also found 6 more pounds of pot inside the house as well as drug paraphernalia such as "packaging materials, scales and smoking devices," California Department of Justice spokeswoman Michelle Gregory said.
Collins released a statement through his attorney on Friday.
"Unfortunately I was just in the wrong place at the wrong time," Collins said in the statement. "However, I do want to take this opportunity to let my fans, friends and family know that I had no part in the reported activities at Jerome's home.
"I have done nothing wrong and I have not been charged with doing anything wrong. So far as I know, I am no longer a part of any investigation."
The case is being investigated by police at the Cincinnati/Northern Kentucky International Airport, along with other local authorities.
Receiver Ted Ginn Jr. was in the 49ers' starting lineup for Braylon Edwards, who had a procedure on his right knee and is out indefinitely. Edwards hurt the knee during an overtime loss to Dallas last week.
Information from The Associated Press and ESPN NFL Insider Adam Schefter was used in this report.