Ian Hume scored a minute into extra time to edge Tranmere past the Premier League side and into a fourth round tie against second division Luton.
Tranmere scored the first goal of the game in the 82nd minute through Eugene Dadi, but Bolton substitute Ricky Shakes equalized in the final minute to force extra time.
In other third round replays, third division Northampton set up a lucrative FA Cup tie with Manchester United by winning its replay 2-1 against first division Rotherham.
Northampton rallied from 1-0 down, with Martin Smith scoring the winner in the 54th minute, setting up another FA Cup meeting with United.
The fourth round will be played on Jan. 24-25. United will travel to Northampton for the match.
In the other replay ties Tuesday, Premier League side Wolves progressed, beating third division Kidderminster 2-0 with two goals from Kenny Miller.
Wolves play West Ham in the fourth round.
Preston beat Reading 2-1 with goals from George Koumantarakis and Richard Cresswell in an all-division one clash. Preston will now face second division Swansea.
Adam Nowland scored as Wimbledon beat fellow first division club Stoke 1-0 to set up a match against Birmingham.
Third division Scunthorpe beat second division Barnsley 2-0 to meet Portsmouth in the next round. Steve Torpey and Jamie McCombe scored for Scunthorpe.
Italian Cup
Marek Jankulovski, Alberto and Sulley Muntari missed scoring chances for Udinese, and Inter Milan escaped with a 0-0 draw at Friuli stadium Tuesday in a first leg match of the Italian Cup quarterfinals.
The Milan powerhouse, coming off a bitter loss to Parma in a crucial league match last Saturday, produced an unimpressive performance as it fielded second-team players to make up for the absence of striker Christian Vieri, midfielder Emre Belozoglu and defender Fabio Cannavaro.
Udinese, which lies seventh in Italy's Serie A, dominated the match for long periods but was unable to turn its supremacy into goals.
Czech midfielder Jankulovski and Brazilian Alberto missed first-half chances while second-half substitute Muntari, a Ghanian midfielder, squandered two consecutive opportunities within four minutes.
Copa del Rey
Ronaldo and Luis Figo netted second-half goals Tuesday as Real Madrid overcame a valiant Eibar 2-0 and advanced to the Copa del Rey quarterfinals on a 3-1 aggregate score.
Madrid suffered throughout the third-round second-leg match as the second-division visitor threatened a shock result but spurned a string of good chances.
Carlos Quieroz's team, lacking injured David Beckham and striker Raul Gonzalez but fielding all its other stars, was forced into some desperate defense by Eibar, which was never overawed by its visit to the Santiago Bernabeu Stadium.
The Basque side, which gained a creditable 1-1 home draw in the first leg, created four goal chances before halftime with striker Gaizka Saizar missing two of them, while Madrid only came close through an early Ivan Helguera header.
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