The suspects, one Kenyan and the other of Somali origin, were planning to attack an unspecified target, they say.
The arrests followed a tip off, a police official added.
Kenya is on a heightened state of alert after militants from Somalia’s al-Shabab Islamist group attacked a shopping centre in Nairobi last year.
Security was increased further following Monday’s incident.
“We have not established where the target was, but we have detained two terror suspects who were in the vehicle,” said Henry Ondiek of the Mombasa Criminal Investigation Department.
“We were tipped off that the two were headed for an attack on an unspecified place and we laid an ambush,” he said.
Two homemade bombs were found in the car along with a mobile phone, which could have been used as a detonator, according to police.
In last September’s attack, at least 67 people died when al-Shabab stormed the Westgate shopping centre.
In February more than 100 people appeared in court in Mombasa accused of being members of al-Shabab, after a raid on a mosque.
Al-Qaeda-affiliated al-Shabab has carried out a series of attacks in Kenya in what it says is retaliation for Nairobi’s decision to deploy troops to Somalia.