For first time in a friendly match against Portuguese national team in 2003, Robben played national championship, three times World Cup tournament, and 3 times in European Cup tournament.
Netherlands needed to win by seven goals to climb above their visitors into second place in Group A but instead finish third on goal difference.
Elsewhere, Portugal secured their place at next summer's World Cup with a 2-0 victory over Switzerland, while Belgium ran out 4-0 winners against Cyprus, with Romelu Lukaku getting in on the act after coming on as a second-half substitute. Spain won 1-0 in extra time.
Arjen Robben took the resulting spot kick and nearly messed up the Panenka finish as the ball dribbled over the line past the outstrecthed boot of goalkeeper Robin Olsen.
As the seconds ticked away toward the final whistle, thousands of fans at the Amsterdam Arena rose to give him a standing ovation, chanting "Arjen, thanks!" in Dutch.
The 33-year-old winger scored both goals for his side in his final Netherlands game.
But Dick Advocaat's side were unable to increase their advantage after the break and will now miss the World Cup in Russian Federation next year, while Sweden will be in the play-off draw on October 17. "We'll miss him, no doubts about that".
"Normally it would be lovely, but it is tough not to go to the World Cup", Robben said, as he ended a career that had many high points on a low.