Star striker Sunil Chhetri put defending champions India ahead when he converted from the spot in the 71st minute in controversial circumstances.
The other three goals were scored by Clifford Miranda (79th), Jeje Lalpekhula (80th) and Sushil Singh (injury time) after Afghanistan were reduced to 10 men following the marching orders by the referee on Afghanistan goalkeeper Hameedullah Yousefzari.
The whole drama started as soon as the referee Sukhbir Singh from Singapore awarded a penalty after Jeje was brought down by Afghanistan central defender Faisal Safa.
The decision was questionable but Afghanistan goalkeeper Hameedullah Yousefzari took things in his own hand by pushing the referee.
The result was a red card which forced the visitors to play with 10 men for the last 20 minutes at Jawaharlal Nehru stadium, which witnessed a turnout of about 5000 spectators, the highest in the tournament.
Afghanistan, who were playing in their maiden final, lost their bearings once their goalkeeper was sent off and India capitalised the advantage to the full.
Afghan coach, Yousef Kargar, was in a quandary as he had to sacrifice a regular player to accommodate his reserve goalkeeper. He brought in reserve goalkeeper Bashir Ahmad at the expense of winger Ghulam Hoddein.
The Indians, meanwhile, regrouped after a mediocre display in the first half. Chhetri, whose first spot kick was disallowed because of intrusion by Nirmal Chhetri, ensured that he was on target after he was asked by retake the penalty.
The strike from the spot and the red card disturbed Afghanistan's momentum and Clifford Miranda scored after receiving a Chhetri through pass eight minutes later. The Dempo winger beat a defender before hitting the target.
Jeje then made it 3-0 when he slammed in after receiving an assist from Chhetri. Substitute Sushil Singh, who came in for Chhetri, rounded off the tally scoring just before the final hooter.
Chhetri finished the tournament with seven goals, the most by any player in this edition of the regional tournament. He was also adjudged player of the match and tournament.
India retained their reputation of being a regional powerhouse intact by lifting the title but they were left gasping for their breath initially.
The first half belonged to Afghanistan as they dominated proceedings by playing attacking football
The Indians were often reduced to mere bystanders and the home side's lack of imagination and inability to control the game was capitalised to the hilt by the Afghans who threatened the Indian goal on many occasions.
The Afghans should have been ahead when dangerman Belal Arezou, who had come into the title clash with six goals to his name, left central defenders Mahesh Gawli and Gouramangi Singh for dead.
Midfielder Yousef Mashriqi did the spadework but Arezou's right-footer was brilliantly blocked by India custodian Karanjit Singh who used his feet to avert disaster for his team.
The Indian goalkeeper deserves a mention as he came to his team's rescue on quite a few occasions.
When Arezou unleashed a powerful shot from the edge of the box, Karanjit was equal to the task making another good save.
Afghanistan, in fact, had a chance in the first minute of the match, as Arezou was on his way after getting the better of Anthony Pereira. It needed a timely intervention from Gouramangi who managed to tackle the dangerous Afghani striker.
Sporting a bandage after suffering an injury on his head, Syed Rahim Nabi, meanwhile, threatened the opposition citadel as he dribbled past three players before failing at the final hurdle.
Before that, a through ball from a midfielder released the nippy Arezou, but Gouramangi just about managed to get his leg in time. But before that, Gouramangi's slack defending almost gave Afghanistan the lead as he failed to clear the ball in his half, and Arezou played the ball which was a bit too far ahead of Sandjar Ahmadi.
But India looked a transformed team in the second session to emerge victorious.
Winners India received a prize purse of USD 50,000 while Afghanistan took home USD 25,000.
In addition, All India Football Federation president Praful Patel announced a cash award of Rs one lakh to each player for winning the tournament.
SAFF Cup: India beat Afghanistan to retain the title
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