Neymar's time at PSG has been hampered by two serious injuries and disciplinary issues, with supporters turning against the man who joined the club for a world record €222 million (£200m/$243m) fee from Barcelona in 2017.
Speaking after Thomas Tuchel's side lost 2-1 away to Rennes in Ligue 1 on Sunday, Silva insisted Neymar remains a vital part of the Parc des Princes dressing room.
The centre-back believes his fellow countryman could still end up remaining at the club, but also concedes that "anything could happen" before the market closes.
"Of course we miss him," Silva told reporters post-match. "I hope that in the end, he will be able to stay with us because he is an incredible guy, an indispensable player for this team but we have to wait for what will happen at the end of the transfer window."
When asked if he thinks Neymar will stay with PSG, the 34-year-old responded: "I cannot answer, but I feel he can stay.
"Neymar is a key player on this team, and he decides if he's happy to stay or not. We do not have to talk, it's always complicated, for a lot of things, we try to talk a little bit about it.
"It is difficult to get into things like that, it's between him and the club right now. We have to wait until the end to see what he decides but I hope that in the end, he will stay. That way we will be much stronger."
Silva also confessed PSG are not as strong in the absence of Neymar, who is still returning to full fitness following an ankle injury suffered just before the Copa America in June.
Barcelona also suffered a loss at Athletic Club this weekend, with Lionel Messi absent due to injury, which Silva referenced when discussing the importance of Neymar.
"It's hard to admit Neymar is missed," he added. "For Barcelona's first match, Messi was also missed. These are different players from everyone else. Neymar can do incredible things, like Messi, like Cristiano [Ronaldo]."
Tuchel has insisted that Neymar will not be sold unless PSG can bring in a suitable replacement, but the club are reportedly open to letting him leave on loan.