The Real Madrid striker also scored his side's third with a thunderous strike and in between played a key part in Noel Valladares' own goal, Benzema's initial shot coming back across goal off the post.
For the first time in World Cup history, goal-line technology was used for confirmation.
Coach Didier Deschamps was delighted with his side's opening gambit in Group E.
"We've had good times during our preparation, but this is competition. Winning today is a very good start," he said.
"We will enjoy this victory, a 3-0 win in the World Cup, because it's never easy. We were patient. We had our chances and hit the bar twice in the first period.
"We did well. Pleasure is total in football when there is victory."
Benzema, making his World Cup bow after missing the cut in 2010, was in high spirits having shot his side to victory.
"I had in mind to play a good game, win while also trying to play my football without pressure. I did tonight," he said.
"I'm very happy and very proud. But the most important thing is winning. Some judge me on my number of goals but, for me, the way I play counts a lot."
Honduras coach Luis Suarez had no complaints about the result, but admitted he was confused by the protocol which initially saw both a 'no goal' and a 'goal' verdict delivered by the GoalControl system following France's second.
The first message related to Benzema's initial shot, while the second covered the Valladares fumble.
''On the second goal, the machine first said that there was no (goal), and after granted one," he said. "I do not know what to think .''
''It was a dream end to the game for us and is very important for the morale of the team,'' Switzerland boss Ottmar Hitzfeld said.
''It will give us some extra strength for the next two matches.
''I really thought this (match-winning) move was delightful. We reacted intuitively and knew how to take advantage of the Ecuadorian mistake.
''It is marvellous to win in the last minute as it releases positive energy.''
Ecuador coach Reinaldo Rueda felt his side were unlucky not to get at least a point.
''It was an intense and evenly matched game. We saw both teams perform to the best of their ability,'' he said.
''We seemed to have the game under control, but what use is that if you end up losing?
''But that's football, although we didn't deserve to lose."
- Sports & Recreation
- Karim Benzema
- Real Madrid
- Didier Deschamps
- Noel Valladares