Joao Pedro scored twice and Moisés Caicedo added a stunning outside-of-the-boot volley as Chelsea controlled the game from start to finish in Jakarta, taking the Brazilian's pre-season tally to five goals.
Joao Pedro glanced home a Caicedo corner in first-half stoppage time to break the deadlock, before doubling his tally moments into the second half from a Pedro Neto cross, and Caicedo capped the win with a driven finish from a Romeo Lavia corner.
Alonso made no changes at the interval, in contrast to AC Milan, who made wholesale substitutions, and the decision paid off as Chelsea struck twice in quick succession after the restart.
Alonso pointed to the fluidity of his side's shape, which shifted in and out of possession with players rotating through the final third, as central to his approach for the season ahead.
"We want to be versatile in our approach and system," he said. "I think we have the players to adapt to different ones because they understand how to support each other.
"The principles are the same but the movements can change; we need to be unpredictable, we want to be flexible, and we want to have a threat. The system is just a picture; you need to move, rotate and create dynamics [in the team] and that is when the picture becomes a movie. We are not just sticking to one idea and the more options that we have, the better team we will be."
He added that the process of building the squad's understanding would continue well beyond pre-season.
"I think that we will get better and by the start of the Premier League season we will be ready. But even that will be another starting point in the evolution of the team. So it will be a process that takes months and in every game."
Marco Palestra was among the standout performers, deployed on the left rather than his more familiar right flank and helping Chelsea keep a clean sheet while also threatening going forward. Alonso praised the Italian's adaptability just a month into his Chelsea career.
"He is having a great impact," the manager said. "He has a hunger and desire to improve and give his best, and in every game he is getting better and better. He played in a different position today, but I knew from his time in Italy he is very flexible and versatile in his game. We are happy he is having such a good adaptation [to life at Chelsea]."
Alonso also thanked the travelling support after the match. "It has been fantastic. The support, cheering us after the game, and even before the kick-off. Our end, the blue end, was really loud. Milan was loud too, so it was a great atmosphere in Jakarta and we want to say thank you because it was a proper atmosphere of football.
"I'm happy our supporters could enjoy the game."
Chelsea's tour concludes on Sunday against Johor Darul Ta'zim in Malaysia.