The Uruguayan forward's efforts lifted Lanus to seven points, two ahead of Brazilians Flamengo.
Regueiro opened the scoring after five minutes, providing the finishing touch to a free-kick from Diego Valeri.
The second goal at the Estadio George Capwell in Guayaquil arrived in the 82nd minute when Mariano Pavone was brought down and Regueiro converted the penalty that followed.
Pavone told Fox Sports: "We knew it was going to be a tough game because we were visitors and Emelec needed a win.
"We are in a good position in the group and I think we'll make it into the next round if we gain 10 points."
In Bolivia, hosts Bolivar claimed a 2-1 win over Colombians Junior to continue their promising campaign in Group Three.
Lorgio Alvarez opened the scoring in the 31st minute and Jhasmany Campos widened the gap through a 39th-minute free-kick strike.
Carlos Ruiz reduced the deficit in the 68th minute but Junior could not find a leveller.
Bolivar had the opportunity to restore their two-goal lead in stoppage-time but Rudy Cardozo's shot hit the right post.
Bolivar lead Group Three with seven points, putting them alongside Union Espanola of Chile, while Chile's Universidad Catolica and Junior are still winless.