Emelec are six points clear of second side LDU Loja, and also have a game in hand - with Gustavo Quinteros' men at their brilliant best on Saturday.
Mondaini struck in the 27th minute, before Angel Mena doubled the champions' lead 12 minutes later.
Alberto Gomez pulled a goal back for Manta early in the second half, but Mondaini had the response for Emelec on 64 minutes to seal their 10th win of the phase in 14 games.
LDU Loja beat Universidad Catolica 1-0 at home, to move clear second in the table.
Byron Calva's goal two minutes prior to half-time was enough for Loja to grab all three points, and sit on 27 for the season - clear of Independiente del Valle (25) and Catolica (24).
Independiente slipped to a third straight loss, as they were humbled 3-2 away at LDU Quito.
Christian Nunez had fired Independiente ahead on 10 minutes, but quickfire goals to Luis Congo and Fernando Hidalgo had them 2-1 up just 14 minutes later.
Hidalgo completed his brace early in the second half, before Jesus Solis pulled a goal back for Independiente, although it would serve only as consolation.
LDU Quito joined fellow bottom-three clubs Mushuc Runa and Deportivo Cuenca in getting on the winners' list.
Bottom club Deportivo Cuenca defeated mid-table El Nacional 3-1 on the road, with goals to Andres Lopez, Juan Cobelli and Eduardo Morante firing the cellar-dwellers to victory.
Mushuc Runa produced a stirring 3-2 win away at Olmedo, coming from two goals down with half an hour to play.
Christian Cordero's three-minute brace drew Mushuc Runa level, before Maximiliano Barreiro struck the winner with six minutes to play.
Barcelona moved fifth courtesy of their third straight win, as they held off Deportivo Quito 1-0.
Flavio Caicedo scored the winning goal for Barca on 52 minutes.
