The network confirmed the end of the project Tuesday night.
Mr. Stewart, the former host of "The Daily Show" on Comedy Central, was brought on in November 2015 to create digital shorts that would appear on the network's digital apps like HBO Now and HBO Go.
But 18 months after signing the deal, the two have agreed to shelve it, saying that the project was significantly more complicated than both sides expected. Mr. Stewart signed a four-year contract, and he will remain at HBO to pursue other efforts.
"HBO and Jon Stewart have decided not to proceed with a short form digital animated project," HBO said in a statement. "We all thought the project had great potential, but there were technical issues in terms of production and distribution that proved too difficult given the quick turnaround and topical nature of the material. We're excited to report that we have some future projects together, which you will be hearing about in the near future."
Even so, the time and investment that were lost are significant.
The digital shorts were expected to roll out some time ago — ideally in conjunction with the presidential election. The goal was to produce a once-a-day release, but as delays set in, HBO executives told Mr. Stewart not to set an arbitrary deadline.
There was also some discussion recently about forgoing the plan to put the shorts on HBO's apps, and instead create a digital strategy that would allow them to be free. The initial plan was to make the shorts two to five minutes long, with Mr. Stewart occasionally providing a voice-over.
"Appearing on television 22 minutes a night clearly broke me," Mr. Stewart said at the time. "I'm pretty sure I can produce a few minutes of content every now and again."
Mr. Stewart was signed at a time when HBO was significantly investing in a variety of unscripted content. But that has led to some fitful starts and stops: Months before Mr. Stewart signed on, HBO announced that it would give Bill Simmons a talk show. That show was canceled after four and a half months. Likewise, HBO introduced a new daily evening show with the media company Vice, but that show has failed to provide moments that have drawn much notice or commentary.
Those deals were made when HBO was also confronting a dry spell with its drama series, a problem that in recent months has become less acute. HBO found success with its new drama, "Westworld" and the limited series "Big Little Lies." Its most popular show, "Game of Thrones," returns in two months for a seven-episode season.
Even with this setback, Mr. Stewart has maintained some presence in show business. In the last year, he has been a regular guest on Stephen Colbert's surging late night show, where he has a credit as an executive producer.