The Australia skipper is now a free agent and will be in big demand in the close season, especially after one of the most impressive seasons in his career.
Viduka, with his two goals in a revenge win over Fulham, brought his tally to 19 goals to finish one of the leading marksmen in the top flight.
The Middlesbrough fans made their feelings clear with a chant of "Sign him on'', during an entertaining finale at the Riverside Stadium.
There has been speculation that Viduka could sign for Portsmouth, but the well-built Aussie could leave his options open, with Newcastle United one of the clubs also after his services.
Boro dominated the early stages but were denied so often by Fulham goalkeeper Antti Niemi. The Finnish shot-stopper was easily Fulham's outstanding player.
Yet he had no chance when Viduka put Middlesbrough ahead with his 18th goal of the season after 34 minutes.
Middlesbrough dominated the first half and it was a surprise when the London side levelled the scores three minutes before the break.
Boro's reserve defender David Wheater saw Simon Davies pounce on his back-header to beat Mark Schwarzer from close range.
Wheater, however, redeemed himself by restoring Middlesbrough's lead in injury time.
After Niemi had denied Fabio Rochemback with a brilliant save, the goalkeeper was beaten by a Wheater header from the resulting corner.
Two minutes into the second half, Viduka demonstrated his close control skill to score from an acute angle before the 29,000 crowd.
When Fulham introduced substitute Franck Queudrue, the defender was given a tremendous ovation by the home crowd, a reflection of the respect in which the Frenchman was held in his five years at the Riverside Stadium.
Fulham had a strong following for the 500-mile round trip to Teesside. Their fans would be disappointed that their side never really looked like achieving their second away win of the season.
New manager Lawrie Sanchez will have some rebuilding to do in the summer if his side are not to be involved in another survival battle next season.
The visitors showed attacking enterprise in the closing stages without troubling Schwarzer.
Overall, a lively and sporting game with only one booking in the 90 minutes. Boro defender Emanuel Pogatetz was shown a yellow card for a foul on Clint Dempsey late in the game.
In the closing minutes Fulham skipper Brian McBride was denied a scoring chance with a Jonathan Woodgate tackle while at the other end substitute Yakubu blasted wide for Middlesbrough.
In the final minutes Viduka was given a standing ovation when he was replaced by Adam Johnson.