Police manning the premises barred the bodyguard from entering the chambers on grounds he was armed.
NASA leaders Raila Odinga and the Bungoma Senator-elect confronted the police demanding the bodyguards be allowed entry.
Raila said they have a right to decide who should accompany them while they are going into the court.
A bodyguard, only identified as Simon, was ejected and held after his gun was withdrawn.
Raila, when he arrived at the court earlier, confronted security officers who did not want him to go in with his security detail.
Trouble started when police officers tried to block part of NASA's entourage from entering the court premises.
Raila was seen having an altercation with one of the officers for about a minute before the NASA team entered the premises.
He was accompanied by chief campaigner Musalia Mudavadi, Kalonzo Musyoka and Vihiga Senator George Khaniri.
The court heard the opposition's submissions in the petition against the declaration of Uhuru Kenyatta as the winner of the August 8 poll.
The judiciary, in an August 25 notice, directed that only police officers deployed in the court premises be armed.
"Kindly note that apart from police officers who are deployed at the courts, no other persons shall be allowed to access our premises with firearms."
This will be the case across the country as the courts prepare to hear petitions around the recent general election.
The judiciary directed that anyone entering the courts will be frisked.
Naivasha chief magistrate Dominica Nyambu directed staff to carry their badges so as to be allowed in court.
"All litigants should deposit their identity cards at the gate before entering the court premises," the notice read.
-The Star| Carole Maina