It seemed that the Sky Blues were going to win for the first time in four outings when substitute Alessandro Matri put them in front late on, only for Zukanovic to intervene and secure a 1-1 draw for the visitors.
During what was a scrappy first half, the only real chance of note fell to Sampdoria when Lazaros Christodoulopoulos's shot at the back post was blocked, with Edgar Barreto unable to turn in the rebound.
The deadlock was eventually broken 12 minutes from the end by AC Milan loanee Matri, who planted his header from Stefan Radu's cross into the top corner of the Samp net.
Bizarrely, while celebrating Matri's goal, Lazio goalkeeper Federico Marchetti suffered a hamstring injury and it proved to be a crucial moment in the game.
In the third minute of added time deputy Etrit Berisha, who had replaced the stricken Marchetti between the posts, hauled down Luis Muriel and from the resultant set-piece situation Zukanovic converted via a deflection off Felipe Anderson.
The draw has moved Lazio up to 12th position in the Serie A standings, while Samp are 16th.