The 32-year-old British and Irish Lion was omitted from Sunday's 23-man squad.
Ferris described his former team-mate as "one of the best try-scorers about".
"Yes he's coming back from a long term injury, but to see him not even involved in such a must-win game was pretty mesmerising for me," Ferris told BBC Radio Ulster on Monday.
"At the same time Les [Kiss] has got to make big decisions at big times and he's doing that."
Bowe suffered a serious knee injury during Ireland's World Cup campaign in October 2015 but has made 11 appearances for Ulster this season.
He came on as a replacement in last week's Pro12 defeat at the Scarlets, having started the New Year's Eve loss at Leinster.
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Ex-Lion Ferris praised Ulster for delivering a much-improved performance against Exeter.
However the defeat has ended their European hopes ahead of Saturday's final pool game at home to Bordeaux-Begles.
Director of Rugby Kiss was frustrated with his team's inconsistencies and failure to finish off opportunities in what was an eighth defeat in the last 12 games.
"It's not working out at the minute," said Ferris, "but Europe is over and in the league there's still a lot of points to play for".
"Let's hope we can get a lot more points and get into the top four and take the positives out of this season.
"Everybody believes Ulster can go well, with home games against so-called easier opposition but then in the last few games we have Ospreys, Leinster and Munster.
"It's going to be a tough run-in but fingers crossed we can pick up a lot of points in the next five or six weeks."
Former Ulster flanker Stephen Ferris has criticised Tommy Bowe's exclusion from the squad in Sunday's European Champions Cup defeat at Exeter Chiefs.