The Eagles got a strong pitching effort from Cameron Cowan and trimmed Northeast Community College, 5-3, at Ashford Field.
Kirkwood (32-18) will face 19th-ranked DMACC (37-15) in the winner's bracket semifinals Friday at noon.
Cowan (3-2) was touched for three runs in seven innings, but all three runs were unearned. He allowed five hits, with seven strikeouts and three walks.
Austin Krob pitched 1 2/3 scoreless inning in relief and Jackson Bennett got the final out for his fifth save.
Northeast scored three times in the bottom of the third inning for a 3-1 lead. Kirkwood pulled within 3-2 in the top of the fourth and grabbed a 5-3 advantage in the fifth with three more runs, knocking Northeast ace Cam Taylor (7-2) out of the game.
Southeastern (39-17) will face Iowa Central (33-18) in the other winner's bracket semifinal Friday in the double-elimination tournament.
Northeast won the season series, 3-1, against Kirkwood this year.
Kirkwood 010 130 000 - 5 9 3
Northeast 003 000 000 - 3 6 2
Cowan, Krob (8), Bennett (9) and Thompson. Taylor, Rodriguez (5), Potter (7) and Weber. W - Cowan (3-2). L - Taylor (7-2). S - Bennett (5). 2B - Pettigrew, Vaske, Thompson. RBI - Jackson, Loston, Thompson. SAC - Brister. SF - Jackson. SB - Usher.