Qualified teams
| Group | Winners | Runners-up |
|---|---|---|
| A |  LionsXII | Johor FC |
| B | Kelantan | ATM |
| C | Negeri Sembilan | FELDA United |
| D | Selangor | Pahang |
The 2012 Malaysia Cup knockout stage will be played from 25 September to 20 October 2012, with the top two teams from every four groups from the group stage advancing to the knockout stage beginning with the quarter-finals followed by the semi-finals and the final. This stage will be played in two legs except for the finals which is played once.
The draw for the group stage was held at Dewan Merak Kayangan, Jalan Semarak, Kuala Lumpur on 2 August 2012 at 17:00 MYT (UTC+8). [1] A draw was made to determine where the teams play while the format of the knockout round remained unchanged.
| Round | First leg | Second leg |
|---|---|---|
| Quarter-finals | 25, 28 & 29 September 2012 | 2 October 2012 |
| Semi-finals | 5 & 6 October 2012 | 11 & 12 October 2012 |
| Final | 20 October 2012 | |
The knockout phase involves the eight teams which qualified as the winners or runners-up of each of the four groups in the group stage.
Each tie in the knockout phase was played over two legs, apart from the final, with each team playing one leg at home. The team that scored more goals on aggregate over the two legs advanced to the next round. If the aggregate score was level, the away goals rule was applied, i.e. the team that scored more goals away from home over the two legs advanced. If away goals were also equal, then thirty minutes of extra time was played. The away goals rule was again applied after extra time, i.e. if there were goals scored during extra time and the aggregate score was still level, the visiting team advanced by virtue of more away goals scored. If no goals were scored during extra time, the tie was decided by penalty shoot-out. In the final, which was played as a single match, if scores were level at the end of normal time, extra time was played, followed by a penalty shoot-out if scores remained tied.
The mechanism of the draws for each round was as follows:
| Group | Winners | Runners-up |
|---|---|---|
| A | LionsXII | Johor FC |
| B | Kelantan | ATM |
| C | Negeri Sembilan | FELDA United |
| D | Selangor | Pahang |
| Quarter-finals | Semi-finals | Final | ||||||||||||||||
| D2 | Pahang | 2 | 0 | 2 | ||||||||||||||
| A1 | LionsXII | 1 | 2 | 3 | ||||||||||||||
| LionsXII | 1 | 1 | 2 (4) | |||||||||||||||
| ATM (p) | 1 | 1 | 2 (5) | |||||||||||||||
| B2 | ATM | 3 | 3 | 6 | ||||||||||||||
| C1 | Negeri Sembilan | 2 | 1 | 3 | ||||||||||||||
| ATM | 2 | |||||||||||||||||
| Kelantan | 3 | |||||||||||||||||
| C2 | FELDA United | 1 | 2 | 3 | ||||||||||||||
| B1 | Kelantan | 2 | 2 | 4 | ||||||||||||||
| Kelantan | 1 | 2 | 3 | |||||||||||||||
| Selangor | 0 | 0 | 0 | |||||||||||||||
| A2 | Johor FC | 1 | 1 | 2 | ||||||||||||||
| D1 | Selangor | 3 | 2 | 5 | ||||||||||||||
The first legs were played on 25, 28 and 29 September, and the second legs were played on 2 October 2012.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Johor FC | 2–5 | Selangor | 1–3 | 1–2 |
| Pahang | 2–3 | LionsXII | 2–1 | 0–2 |
| ATM | 6–3 | Negeri Sembilan | 3–2 | 3–1 |
| FELDA United | 3–4 | Kelantan | 1–2 | 2–2 |
| Selangor | 2–1 | Johor FC |
|---|---|---|
|
Selangor won 5–2 on aggregate.
| Pahang | 2–1 | LionsXII |
|---|---|---|
|
| LionsXII | 2–0 | Pahang |
|---|---|---|
|
LionsXII won 3–2 on aggregate.
| ATM | 3–2 | Negeri Sembilan |
|---|---|---|
|
| Negeri Sembilan | 1–3 | ATM |
|---|---|---|
|
ATM won 6–3 on aggregate.
| FELDA United | 1–2 | Kelantan |
|---|---|---|
|
| Kelantan | 2–2 | FELDA United |
|---|---|---|
|
Kelantan won 4–3 on aggregate.
The first legs were played on 5 & 6 October, and the second legs were played on 11 & 12 October 2012.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| LionsXII | 2–2 (4–5 p) | ATM | 1–1 | 1–1 (a.e.t.) |
| Kelantan | 3–0 | Selangor | 1–0 | 2–0 |
| ATM | 1–1 (a.e.t.) | LionsXII |
|---|---|---|
|
| |
| Penalties | ||
Marlon  Aidil  Rezal Reuben Martelotto Varanthan Fitri | 5–4 | Khairul Shahdan Hariss Shaiful Izwan Baihakki Yasir |
2–2 on aggregate. ATM won 5–4 on penalties.
| Selangor | 0–2 | Kelantan |
|---|---|---|
Kelantan won 3–0 on aggregate.
The final will be played at the Shah Alam Stadium in Shah Alam, Malaysia on 20 October 2012.
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