Shiel played just three games after round nine and none after round 17, with the foot injury hampering his ability to get out on the park.
The 30-year-old's name was floated as a possible trade option before Wednesday's deadline and he underwent surgery on Thursday in a bid to be fit for the 2024 campaign.
It came just weeks after he underwent minor knee surgery.
"Dylan's foot hasn't fully recovered post season and his conservative rehab approach hasn't provided pain relief for him," Essendon football manager Dan McPherson said in a statement.
"After consulting a surgeon in the last few days, it was decided that further intervention was required to allow him the best chance to return to training and playing pain-free.
"Dylan is the ultimate professional who will be relentless in his pursuit to return to full training as early as possible.
"He will be off-legs for a couple of weeks and will then begin reloading progressively over the pre-Christmas period."
Shiel joined the Bombers from GWS on a six-year deal at the end of 2018.
The 211-game veteran has been limited to just 39 matches across the past three seasons and Essendon will be hoping the former Giant can now put his injury woes behind him.
The news on Shiel came just a day after Essendon secured former Port Adelaide midfielder Xavier Duursma during the trade period.
The 23-year-old was traded to Essendon in exchange for defender Brandon Zerk-Thatcher, pick No.73 and two future fourth-round picks.
Can't wait for you to don the sash, X! — Essendon FC (@essendonfc) https://t.co/z4YRtTzVEc pic.twitter.com/qTbIPSSV3VOctober 19, 2023
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