The coach rested Gareth Bale, Marcelo and Toni Kroos, handing a debut to defender Alvaro Odriozola in place of the injured Dani Carvajal.
Modric played a major role in Madrid's third successive Champions League success and Croatia's journey to the World Cup final in Russian Federation, winning the Golden Ball in the process.
Real Madrid president Florentino Perez has ruled out the possibility of the club featuring in a La Liga fixture in the United States. "I don't know in whose interest it [a game in the U.S.] is, but is not in the interests of the clubs and the fans".
Marco Asensio celebrates his winner
"We have to defend the title and it's always a bit more motivation when the final is in Madrid, the home of an opponent like Atletico", the defender said.
"Espanyol played well and were organised, and we knew it would be hard", said Lopetegui, who remains unbeaten in LaLiga since replacing Zinedine Zidane in the summer.
The Whites had a few headaches to worry about on the night, majority being from a defensive point of view.
Madrid's next Champions League clash comes against CSKA Moscow at 3 p.m. on October 2 at VEB Arena in Moscow.
"Ten is a number that I like, but it's in the hands of Modric".
"We lacked energy in the second half and lost control".
Roma may head to Spain on the back of just one Serie A win - and that on the opening weekend of the new season - but Lopetegui is expecting a stern test from the Italians. "They're working very well".
"As a coach, he has entered the history books as a giant of Real Madrid".
"They haven't told me anything to change the number and that's why I haven't been able to decide either", he said. 'These post-Champions League games are always really risky and we know it'.
Both men could see their paths cross with Real again at some stage in the near future, with it possible that Champions League competition could deliver emotional reunions.