Jeje scored India's fourth after being fed by Chhetri in the dying minutes.
However, the hosts conceded in the 37th minute when Nicholas Tarrao scored.
In the 2011 edition that was held in Doha, India lost all their group matches to Australia, South Korea and Bahrain.
India opened the account in the 28th minute, when Borges's side-footer deflected off Macau defender Ieong Cheng and past the custodian.
Amidst the successful hosting of the FIFA U-17 World Cup 2017 where the India U-17 football team are winning hearts of 1.3 billion people with their stupendous performances, the senior Indian national football team made matters brighter for the handsome game in the country by qualifying for the AFC Asian Cup UAE 2019 on Wednesday October 11.
The Indians made their domination count when Narayan Das fired in a low cross from the left wing which was met by a Jeje backheel. Torrao then stole the ball before it could reach Pritam Kotal and headed it in to draw level. Chetri put India ahead 2-1 after he capitalised on a sloppy defensive play. However, before the Indian skipper could capitalise with the ball at his feet in the box, Macau goalkeeper Ho Fai smothered it. Jeje took it in near the halfway line and sent Balwant clear.
Balwant clearly had an impact on the game as his clever running of the channels had the Macanese defenders scampering all over and India started to find a lot of space.
India were lucky to have got the third strike through a self goal after Lam Seng's attempted clearance turned into disaster as the ball looped over the goalkeeper and went in. Earlier, they had beaten Myanmar 1-0, Kyrgyz Republic 1-0 and Macau 2-0.
India kept creating chances as they searched for the opening goal.
This will be India's fourth appearance in the Asian Cup finals.
"I was there when we missed out in 2015 and that still hurts me".
Asia Cup is scheduled to take place in 2019 and India have 2 long years at their bay to prepare for the elite competition which will feature the best of Asian sides. This is the tournament we play for.
Chetri lauded his teammates for their performance. We need to work harder because things will get difficult for us now that we are a qualified team. This is indeed a quick change in fortunes for the national team which had a disastrous 2018 FIFA World Cup qualifying campaign losing all but one of their eight games. Till then it was mostly one-way traffic - in pouring rain - as Macau battled hard to keep the Indians at bay.