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Bolton also finished with ten men, as Ivan Campo was sent off for a second yellow card.
Seaman's embarrassment came in the wake of Ronaldinho's long distance World Cup winner for Brazil and Gianfranco Zola's speculative free-kick in the 1-1 draw at Chelsea.
But Arsenal boss Arsene Wenger defended his goalkeeper. He said: "It was a freak. I don't think any keeper could save that." He added: "It was a hard-earned win. We had to show all our spirit, but we deserved it in the end."
The goals by Kanu and Henry also ensured that Arsenal equalled Chesterfield's 72-year-old record of scoring in 46 consecutive league games.
Bolton, who recently won 1-0 at Manchester United, looked grabbing a point until Kanu struck, prodding home from close range after Henry flicked on a cross.
The visitors played the last 11 minutes a man short after Campo, already booked for dissent, was dismissed by referee David Pugh for throwing the ball away at an Arsenal free-kick.
Bolton boss Sam Allardyce said: "This is the second week running that we've been beaten in the final minute. The players are distraught after a magnificent effort."
Henry could have had a hat-trick. His 13th-minute penalty beat keeper Jussi Jaaskelainen, but crashed against a post, then he had a second-half strike disallowed for a debatable offside.
Kanu and Sylvain Wiltord had shots blocked too as the champions pressed for a winner