Jones hit 7 of 17 from the field as the Gaels (17-13, 11-7) shot 50 percent (33 of 66), including 8 of 23 from 3-point range. Taaj Ridley added 14 points and nine rebounds, while David Laury had 13 points and Sean Armand 11.
Iona had 25 assists to just 10 turnovers, while Siena had 14 helpers and 20 giveaways.
O.D. Anosike led Siena (7-23, 4-14) with 17 points. The Saints have lost 19 of their past 21 road MAAC games.
With the win, Iona earned the fourth seed in the MAAC tournament and will face fifth-seeded Canisius at 4:30 p.m. on Saturday.
Siena will be the ninth seed and face eighth-seeded Marist on in the first round Friday at 7:30 p.m.