The former Barcelona star was not available to manager his country due to family reasons. However, despite not being on the sidelines, the 2010 World Cup winners cruised to victory with a brace from Álvaro Morata.
“First of all, I want to give my support to Spain coach Luis Enrique and his family,” Farrugia said.
“I wish that things get better for him because this is more important than a football game.
“I spoke to his assistant coach (Robert Moreno) and told him to convey my thoughts to Mr Enrique and his family.”
The Malta boss continued by praising Spain for their impressive performance at the Ta’Qali National Stadium as they came out 2-1 winners.
“We were playing against one of the best teams in the world,” the 63-year-old said.
“Although we suffered, the possession was 80 per cent for Spain and 20 per cent for us – I believe it was more or less the same when Spain played Norway last Saturday – I think tactically we were really good.
“We could have avoided the first goal. Apart from that, Spain didn’t create a lot of chances. Spain
Farrugia finished by speaking about the inclusion of young players in Malta’s squad during their opening qualifier games.
“There is room for improvement plus the fact that we are introducing more young players,” said the Malta boss.
“As I told you, in the present moment we will suffer a bit until we get them (young players) going and they understand better what we want from them, but the future looks bright.”