Essebsi, from the Nidaa Tounes party, got 39.46 percent in Sunday's poll, short of the needed overall majority but ahead of Marzouki, who got 33.4 percent, according to the figures.
The vote for Tunisia's first directly-elected president marks the final step in the North African state's transition to full democracy following a 2011 revolution that ousted long-time ruler Zine el-Abidine Ben Ali.
Essebsi is a former Ben Ali official and Marzouki had depicted the race as a chance for voters to reject the old guard, Reuters reported.
More than three years since overthrowing Ben Ali's one-party rule, Tunisia adopted a new constitution, and rival secularists and Islamist parties have largely avoided the turmoil that has plagued other Arab states swept by popular revolts.