Playmaker Riquelme scored his first goal for Boca since his comeback from an eight-month sabbatical, lifting the Argentine side into second place in Group One, a point behind Nacional.
In a tight group, Uruguayans Nacional have seven points, Boca six, Toluca of Mexico five and Ecuador's Barcelona three. There have been no home wins in the eight matches so far.
Boca, who also beat Barcelona in Guayaquil but have lost twice at home, were on top at the Centenario before defender Claudio Perez brought down Nacional midfielder Juan Albin in the box midway through the first half.
Perez, who had been booked early on, was sent off and Nacional were awarded a penalty. However, Ivan Alonso wasted the chance to put his team ahead by blasting the ball over the bar.
With two minutes of the half remaining Boca were awarded a penalty of their own when Nacional defender Andres Scotti brought down striker Juan Manuel Martinez and Riquelme converted the spot-kick.
It was a Boca record 24th goal for Riquelme in the Libertadores Cup, surpassing the 23 scored by former striker Martin Palermo.
Boca left-back Clemente Rodriguez played an Argentine record 77th match in the tournament, which he has won three times.
