It was the fastest ever goal in a World Cup qualifier.
The Crystal Palace striker stole the ball in the home side's half straight from the kickoff and weaved his way through Gibraltar's defence to score from inside the area.
Benteke celebrated the record-breaking strike, also the fastest goal scored by a Belgium international, by holding up six fingers, thinking he had scored after six seconds.
Axel Witsel scored from 25 metres after 19 minutes to double Roberto Martinez's side's advantage and Benteke scored his second shortly before halftime when he turned in Thomas Meunier's cut back from six yards.
After Dries Martens scored the fourth with a dinked finish in the 51st minute Benteke completed his first hat-trick for Belgium five minutes later with a backheel from Eden Hazard's pass.
Chelsea forward Hazard then added to his assist by completing the rout in the 78th minute.
Belgium top Group H on nine points thanks to their superior goal difference over Greece, who also extended their 100 percent start by winning 2-0 in Estonia.
"The fact we scored so early proves we were fully concentrated," Martinez told newsmen.
"We weren't selfish, we played for each other. Our aim was to score early to make our job easier and that's what we did. I'm very pleased with the display we put on."
Martinez also said Benteke's return to form for club and country was his reward for working hard to try and bounce back from an underwhelming last year with Liverpool.
"As well as scoring he held the ball up really well," added Martinez on Benteke, who has scored three goals in five Premier League appearances for Crystal Palace.
"He has been rewarded for all the hard work in recent weeks. He had a difficult last season and is trying to find his best form again."