Babar Azam, No.1 batsman in T20Is, also went unsold. Kieron Pollard, Dwayne Bravo, Quinton de Kock and Tamim Iqbal were the other big names were missing.
Both Gayle and Malinga had set their base price at the maximum of 125,000 pounds, along with Mitchell Starc, Steve Smith, David Warner and Kagiso Rabada and that meant that they had to be bought in the first round of the draft, reports the ICC.
While Starc and Smith were bought by Welsh Fire, Warner was taken by Southern Brave. However, Gayle, Malinga and Rabada all missed out on selection.
"Excited to be joining the Welsh Fire in #TheHundred next year. Can't wait!" tweeted Smith.
Afghanistan's star leg-spinner Rashid Khan was the first pick and was picked by Trent Rockets. He will play alongside England Test captain Joe Root, who described him as "one of the best players in the world".
The other big names to go in the first round were Andre Russell (Southern Brave), Aaron Finch, Mujeeb Ur Rahman (both Northern Superchargers), Sunil Narine (Oval Invincibles), Imran Tahir, Dane Vilas (both Manchester Originals), Glenn Maxwell (London Spirit), and Liam Livingstone (Birmingham Phoenix).
There were seven salary brackets -- 125,000, 100,000, 75,000, 60,000, 50,000, 40,000 and 30,000 pounds -- that made for the seven rounds of two picks each.
A total of 570 players were there in Sunday's men's draft, including 239 overseas players and 331 domestic players. In total 96 players were selected in the first major player draft and 474 went unsold.
The Hundred is a 100-ball format that is set to launch in July next year with the men's and women's tournaments to run concurrently over a five-week period.