The result left the two-legged contest level at 3-3 on aggregate, but San Pedro advanced to the next round on the away-goals rule, bringing Rivers United's continental campaign to a disappointing early end.
• Rivers United: 2 goals
• San Pedro: 2 goals
Rivers United went into the decisive encounter with the tie finely balanced after securing a 1-1 draw in the first leg in Côte d'Ivoire.
The Nigerian champions therefore needed a victory in Uyo to guarantee their passage to the next round. However, San Pedro stunned the home supporters by establishing a two-goal lead in the first half.
Rivers United responded strongly after the interval, throwing more players forward and increasing the pressure on the visitors.
Their persistence eventually paid off as the Pride of Rivers scored twice to draw level at 2-2, setting up a tense finale in Uyo.
However, despite their impressive fightback, Rivers United could not find the winning goal they needed.
San Pedro held firm through the closing stages to secure qualification, leaving the Nigerian side to rue a first-half collapse that ultimately proved decisive.
Away goals send San Pedro through
With the first leg ending 1-1 and the return leg finishing 2-2, the aggregate score stood at 3-3.
San Pedro progressed because of the away-goals rule, having scored twice in Uyo compared with Rivers United's single away goal in the first leg.
The elimination is a major disappointment for Rivers United, who had hoped to make a strong impression in Africa after winning their opening 2026/27 NPFL fixture 2-0 against Plateau United.
Their continental campaign, however, has ended after just two matches against San Pedro, with both encounters finishing in draws.
Rivers United must now turn their attention back to domestic football, while San Pedro advance to the next stage of the CAF Champions League.
For the Pride of Rivers, the comeback in Uyo showed character, but their inability to recover from the two-goal deficit proved costly as San Pedro survived 3-3 on aggregate and progressed on away goals.