Sevilla frustrated Madrid for long spells of the contest, but Casemiro's stunning hit in the 78th minute and Modric's late effort moved Los Blancos above their opponents on the afternoon into third spot in the table.
The visitors settled as the first half progressed, however, with Jesus Navas causing Madrid problems in the wide positions as Sevilla's wing-backs became more involved.
Vinicius was Madrid's best player against Leganes in the Copa del Rey on Wednesday night and the Brazilian was again the individual making things happen for Los Blancos in the final third.
Madrid arguably shaded the overall play in the first half of action, but Sevilla had the better chances to make the breakthrough and the Bernabeu was not too happy at the half-time interval once again.
Karim Benzema was declared fit to start despite suffering a fractured finger against Real Betis last weekend, but the France international found it difficult to contribute in the first 45 minutes and the same can be said for Lucas Vazquez and Dani Ceballos.
Vinicius flashed an attempt wide of the Sevilla post in the 52nd minute, before Casemiro missed from outside the box moments later with Madrid the team on the front foot at the start of the second period.
Modric was next to try his luck for the home side just before the hour, but his effort was deflected behind. Madrid were dominant, although they were struggling to find that final piece of quality in attack.
Vinicius poked one wide of the Sevilla goal 25 minutes from time, before Ceballos rattled the crossbar with a wonderful strike in the 67th minute.
Casemiro was next to come close as the Brazilian headed just wide of the Sevilla post in the 74th minute, moments before Munir El Haddadi replaced Andre Silva in the away side's attack.
The out-of-form Isco replaced Vazquez in the 77th minute and less than one minute later Madrid were ahead.
Casemiro had threatened with a couple of headers in the second period and the Brazilian sent his team ahead in the 78th minute with a stunning long-range attempt which was too powerful for Vaclik to handle.
Madrid - now seven points off leaders Barcelona - then made sure of the points in second-half stoppage time when Modric robbed the ball from Daniel Carrico before firing into the back of the net.
REAL MADRID (4-3-3): Courtois; Carvajal, Varane, Ramos, Reguilon; Ceballos (Valverde 88'), Casemiro, Modric; Vinicius, Benzema, Vazquez (Isco 77')
SEVILLA (3-4-1-2): Vaclik; Carrico, Kjaer, Gomez; Navas, Banega, Vazquez, Escudero (Gil 86'); Sarabia; Ben Wedder (Promes 72'), Silva (Munir 74')