Ban called Kibaki to express his hope that Kenyans would put interests for peace on display at the polls.
"The secretary-general expressed appreciation for efforts made to strengthen Kenya's democracy and its electoral system since the last general elections," a statement from Ban's spokesman read.
"He trusts that efforts made at many levels to prevent a repeat of past violence will be redoubled during the remainder of the campaign."
The United Nations and the human rights community have expressed concern that a cycle of violence may repeat itself during the election.
Thousands of people were killed following 2007 elections amid clashes between supporters of Kibaki and challenger Raila Odinga.
A Kenyan court this month cleared Deputy Prime Minister Uhuru Kenyatta and his running mate, William Ruto, to run in the Monday election. Both men could face charges at the International Criminal Court for crimes related to conflicts after the 2007 elections.
Monday's election is the first under a new constitution that sought to enact reforms following the post-election crisis.