The vote reflected public discontent with Abbas and his Fatah movement, whose popularity has sunk due to a weak economy, nepotism in its ranks and its failure to lead the Palestinians closer to independence.
Saturday's vote gave Palestinians a rare chance to cast ballots after over a decade without presidential or legislative elections. Abbas' embattled party ran virtually unopposed, and Saturday's election was seen as a litmus test of Fatah's popularity.
But the results indicated lackluster support for the party, which has dominated Palestinian politics for half a century. In an indication of public sentiment, just 53 percent of eligible voters cast ballots. Voter turnout in the previous municipal elections, in 2012, was comparable, elections commission director Hisham Khalil said.
In Hebron, the West Bank's largest city and a Hamas stronghold, Fatah won just seven of 15 seats.
"The result wasn't great for us," said Tayseer Abu Sneineh, the head of Fatah's list in the city.
In Nablus, another major city, Fatah won 11 of 15 seats, but only after forming an alliance with Islamist candidates. Turnout in Nablus was just 21 percent.
Fatah only won clear victories in two major cities, Jenin and Jericho. In several cities, Fatah couldn't piece together enough candidates to field a campaign list, leaving local Fatah politicians to run as independents.
Roughly 2.2 million Palestinians live in the West Bank, of whom just over 787,000 were eligible to vote. East Jerusalem's 300,000 residents didn't take part in the elections.
The Palestinians have been divided between rival governments since Hamas defeated Fatah in the 2006 legislative elections and drove the latter out of the Gaza Strip the following year, leaving Abbas in control only of the Palestinian Authority autonomy government in parts of the West Bank. Repeated attempts to reconcile have failed.
Fatah and Hamas were supposed to compete in elections last year in both the West Bank and Gaza. But with the rival factions disqualifying each other's candidates, Fatah went forward with the elections in the West Bank alone in a bid to renew its legitimacy.
The Palestinian president is currently more than a decade into what was supposed to be a four-year term.
Hanna Nasser, head of the Central Elections Commission, said the organization plans to approach Hamas about the possibility of holding municipal elections in the Gaza Strip.