Howell shot 4-under-par 68 and tied for second after taking a brief lead in the final round of the Zurich Classic of New Orleans.
Jerry Kelly shot 71 and finished at 14-under 274 to earn his third career win on the PGA Tour.
Howell, Rory Sabbatini (67) and Charlie Wi (68) finished a shot back.
Howell was 5 under on the front nine to take the lead. He held a one-shot lead over Kelly, who led after 54 holes.
Howell missed out on this year's Masters for the first time since 2002.