The two-time champion will get a 30-place grid penalty for using more than the permitted number of engine parts.
Reliability problems mean Alonso needed the engine to complete the season, but it also has upgraded parts.
The new power unit has a lighter engine block for better reliability and a redesigned exhaust to boost efficiency.
Alonso, 35, will run the new engine in first practice on Friday before Honda decides whether to keep it in the car for the second session.
"We had a plan at the middle of the season which races were the best ones to pay the penalties," said Alonso.
"This one was one of the best because the conditions change here and the rain may come, and also Suzuka is the next one and we want to do a good job there because it is the home grand prix.
"So it was one of the best races to go for the rest of the season with a little more confidence. And the last time I started last in Spa I was fifth or fourth after five laps, so maybe in this weekend I am lucky as well."
At this stage, Honda is planning to run the engine only on Friday, with Alonso switching back to the same specification as team-mate Jenson Button for the rest of the weekend. But it is not impossible the Spaniard will run the new engine for qualifying and the race as well.
The new parts mean Alonso will be using his eighth internal combustion engine, turbocharger, and MGU-H - the part of the hybrid system that recovers energy from the turbo - and his seventh control electronics, and energy store (battery).
The only part of his engine carried over from previous races is the MGU-K, which recovers energy from the rear axle.
If everything goes to plan, Alonso will use the new engine for the entire Japanese Grand Prix meeting next weekend.
At this stage, Honda is not planning for Button to use it in Suzuka because it does not want any grid penalties at its home race.
Drivers are permitted to use only five of the six constituent parts of the engine without incurring a penalty.
McLaren's Fernando Alonso will start Sunday's Malaysian Grand Prix from the back of the grid because he is to test an updated Honda engine.