The seamer was not selected in the 15-man group for the global tournament, that will start on 7 February, despite being the top wicket-taker across the four seasons of South Africa's premier domestic competition.
The selectors opted for international experienced campaigners in the fast bowling contingent with Kagiso Rabada, Lungi Ngidi, Anrich Nortje all making the squad.
Corbin Bosch and Kwena Maphaka were selected ahead of Baartman as the duo offer more pace, but Baartman has shown he can be deceptive with his wider variations.
The 32-year-old has thrived under the captaincy of Proteas batter David Miller, who is in the T20 World Cup squad, at the Paarl Royals this season with 11 wickets in his first four matches.
Baartman is also the senior paceman in the Royals' team with 19-year-old Nqobani Mokoena already picking up seven wickets in his maiden SA20 campaign.
Miller offered encouraging to words to Baartman as the T20 World Cup, which will be held in India and Sri Lanka, draws closer.
"It's obviously hard on guys," Miller said. "I've been in that position back in the day, not making a World Cup, being a part of the team and then missing out, and it's a bit of a blow.
"Unfortunately, there's only a squad of 15. At the end of the day, it is what it is. The response is, for me, the biggest thing. How guys come back. It's a big tournament and you never know, there's potentially injuries.
"So you always want to keep your head up and keep doing the right things. He's definitely done that. He's come out and really performed, put all that aside."
Baartman will be looking to continue his good form when the Paarl Royals take on Joburg Super Kings at the Wanderers on Thursday.
Shai Hope and Lungi Ngidi delivered landmark performances as Pretoria Capitals beat Durban's Super Giants by 15 runs in a dramatic SA20 clash at Kingsmead.
MI Cape Town recorded their first win of the SA20 season after a four-wicket victory against Joburg Super Kings in a match that was reduced to 12 overs per side due to rain at Newlands.
Dale Steyn has questioned South Africa's decision to leave Ottneil Baartman out of their T20 World Cup squad, despite the pacer's outstanding form in the SA20.
Jason Smith says he will bring versatility to the Proteas batting order after being included in the squad for the T20 World Cup that will start on 7 February and will be co-hosted in India and Sri Lanka.
