The 2008–09 CONCACAF Champions League championship round began on 24 February 2009. The draw for the championship round was held on 10 December 2008. In each round, teams will play their opponent once at home and once away. The four group winners from the group stage will play the second leg at home in the quarterfinals. The order of the home and away matches for the semifinals and finals were determined in the draw.
In all rounds, if two teams are tied after both legs the team with the most away goals is the winner. If the two teams are also tied in away goals, then two fifteen-minute halves of extra time are played. If the two teams are still tied in total goals after extra time, a penalty shootout determines the winner.
Bracket
| Quarterfinals | Semifinals | Finals | |||||||||||||||
 Puerto Rico Islanders
| 2 | 1 | 3 | ||||||||||||||
.svg.png.webp){kind=small} Marathón
| 1 | 0 | 1 | ||||||||||||||
| Puerto Rico Islanders
| 2 | 1 | 3 (2) | ||||||||||||||
 Cruz Azul (p)
| 0 | 3 | 3 (4) | ||||||||||||||
| Cruz Azul
| 1 | 1 | 2 | ||||||||||||||
| UNAM
| 0 | 0 | 0 | ||||||||||||||
| Cruz Azul
| 0 | 0 | 0 | ||||||||||||||
| Atlante
| 2 | 0 | 2 | ||||||||||||||
.svg.png.webp){kind=small} Montreal Impact
| 2 | 2 | 4 | ||||||||||||||
| Santos Laguna
| 0 | 5 | 5 | ||||||||||||||
| Santos Laguna
| 2 | 1 | 3 | ||||||||||||||
| Atlante
| 1 | 3 | 4 | ||||||||||||||
 Houston Dynamo
| 1 | 0 | 1 | ||||||||||||||
| Atlante
| 1 | 3 | 4 | ||||||||||||||
Quarterfinals
The first legs of the quarterfinals were played from 24 February 2009 to 26 February 2009, while the second legs were played from 3 March 2009 to 5 March 2009.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Houston Dynamo |
1–4 | Atlante |
1–1 | 0–3 |
| Montreal Impact |
4–5 | Santos Laguna |
2–0 | 2–5 |
| Puerto Rico Islanders |
3–1 | Marathón | 2–1 | 1–0 |
| Cruz Azul |
2–0 | UNAM |
1–0 | 1–0 |
First leg
| Houston Dynamo | 1–1 | Atlante |
|---|---|---|
Boswell  30' |
(Report) | Pereyra 82' |
| Montreal Impact | 2–0 | Santos Laguna |
|---|---|---|
| Sebrango 5', 77' |
(Report) |
| Puerto Rico Islanders | 2–1 | Marathón |
|---|---|---|
| Addlery 74' Jagdeosingh 80' |
(Report) | Palacios 41' |
Second leg
Atlante won 4–1 on aggregate.
| Marathón | 0–1 | Puerto Rico Islanders |
|---|---|---|
| (Report) | Addlery 90' |
Puerto Rico Islanders won 3–1 on aggregate.
Cruz Azul won 2–0 on aggregate.
| Santos Laguna | 5–2 | Montreal Impact |
|---|---|---|
| Benítez 16' Vuoso 52', 75'Quintero 90+2', 90+5' |
(Report) | Brown 24' Sebrango 38' |
Santos Laguna won 5–4 on aggregate.
Semifinals
The first legs of the semifinals were played on 17 March and 18 March 2009, while the second legs were played on 7 April and 8 April 2009.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Puerto Rico Islanders |
3–3 (2–4 p) | Cruz Azul |
2–0 | 1–3 (a.e.t.) |
| Santos Laguna |
3–4 | Atlante |
2–1 | 1–3 |
First leg
| Puerto Rico Islanders | 2–0 | Cruz Azul |
|---|---|---|
| Gbandi 4' Addlery 37' |
(Report) |
| Santos Laguna | 2–1 | Atlante |
|---|---|---|
| Quintero 6', 75' |
(Report) | Pereyra 35' |
Second leg
| Cruz Azul | 3–1 (a.e.t.) | Puerto Rico Islanders |
|---|---|---|
| Zeballos 44' Orozco 84'Villaluz 99' |
(Report) | Gbandi 92' |
| Penalties | ||
Zeballos  Andrade Torrado Lugo  Orozco |
4–2 | Arrieta Delgado Jagdeosingh Krause |
3–3 on aggregate. Cruz Azul won 4–2 on penalties.
Atlante won 4–3 on aggregate.
Final
The two-legged final was played on 22 April and 12 May 2009. The second leg was originally scheduled for 29 April, but was postponed until 12 May by CONCACAF due to concerns over an outbreak of swine flu in Mexico.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Cruz Azul |
0–2 | Atlante |
0–2 | 0–0 |
First leg
Second leg
| Atlante | 0–0 | Cruz Azul |
|---|---|---|
Atlante won 2–0 on aggregate.
| CONCACAF Champions League 2009 Champion |
|---|
|
| Atlante Second Title |