The 26-year-old American streaked home in an impressive 12.98sec, finishing far ahead of the rest of the field after a dynamite start.
European silver medallist Enrique Llopis of Spain booked the other automatic spot from the first of three semis in 13.17sec.
"I felt great," said Holloway, who is also the two-time world indoor 60m champion and world 60m record holder.
"It wasn't the best race I've run this year, but I'll take it. I'm in the Olympic final, so looking forward to that and seeing what I can do."
Jamaican Hansle Parchment, the defending Olympic champion, scraped into the final as one of the next two fastest qualifiers after he only finish third in 13.19sec. Japan's Rachid Muratake was the other beneficiary.
"It wasn't a very good run," said Parchment. "It was good enough to advance.
"So now I am just refocusing on seeing how I can do better in the next one."
Holloway will be joined in the final, scheduled for 1945 GMT on Thursday, by two other Americans, Freddie Crittenden and Daniel Roberts.
Crittenden came in second behind Jamaican Rasheed Broadbell, the winner of the second semi in 13.21sec.
Roberts came in on the coattails of Jamaican Orlando Bennett, who won the third semi in 13.09sec.
