The Tour of the Alps five-stage race was Meintjes' final preparation event ahead of his Giro d'Italia debut.
Dumoulin was happy with the start to the tour.
Froome suffered cuts and grazing and duly completed the 9.7-kilometre route 37 seconds slower than Dumoulin, who clocked a time of 12 minutes and two seconds to take the Maglia Rosa.
The Dutchman from Team Sunweb was the last of the 175 riders to start.
The prestigious race is being held outside Europe for the first time in its 101-year history.
Desktop Chrome Now Sports Autoplay Muting
The company is now improving its autoplay blocking by learning the preferences of a user, based on their browsing history. As you navigate online using Chrome, it will progressively learn which sites you enable sound on, and which you don't.
The individual time trial course is a technical affair around the twisting and turning roads of Jerusalem, Israel. Last year, he entered the final stage in Milan in fourth but surged to victory.
The third fastest man on a warm and sticky day was Belgium's Victor Campenaerts, only a fraction of a second slower than Dennis, with Portugal's Jose Goncalves fourth, 12 seconds back. "To have the win and time on the other GC guys is a pefect start for me and the team." said Dumoulin. "I knew I was ready for the Giro but I wasn't sure I'd win today".
"This is flawless, it's all I wished for".
Since making his Grand Tour debut in 2014, Meintjes has two 8th place finishes at the Tour de France and a top 10 at the 2015 Vuelta a España.
The second leg of the race stretches 167 kilometers (104 miles) down the Mediterranean coast from Haifa to Tel Aviv.
The race will then transfer to Italy, and the island of Sicily, for an early rest day on Monday. The Giro ends in Rome on May 27.