Howe watched the Magpies' 4-1 win over Manchester United on Sunday from his hospital bed after being admitted on Friday evening having been feeling unwell for several days.
Newcastle have now said the 47-year-old will also miss Wednesday's home match against Crystal Palace and Saturday's trip to Aston Villa, with assistant Jason Tindall and Graeme Jones due to prepare the team in his absence.
"Newcastle United can announce that Eddie Howe is recovering in hospital after being diagnosed with pneumonia," a statement read. "The club continues to extend its best wishes and support to Eddie and his family as he continues his recovery.
"Jason Tindall and Graeme Jones will lead the team against Crystal Palace and Aston Villa this week, with further updates to be communicated in due course."
Howe, who sent his congratulations to the team after Sunday's impressive win over United moved them back into the top four, offered thanks for the messages of support he has received.
"A huge thank you to everyone connected with Newcastle United and the wider football community for your messages and warm wishes. They have meant a lot to me and my family," Howe said.
"I also want to pay tribute to our incredible NHS and the hospital staff who have treated me. I'm immensely grateful for the specialist care I'm receiving and, after a period of recovery, I look forward to being back as soon as possible."
Newcastle will move above Nottingham Forest into third place if they avoid defeat against Palace at St James' Park.
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