The duo made the difference following their introduction from the bench after Antoine Griezmann had seen a goal correctly ruled out for offside by the Video Assistant Referee (VAR), which was deployed in successful fashion in Saint-Denis.
Both teams named strong starting XIs for the encounter, with France handing a first start to rising Monaco star Kylian Mbappe and a debut for Corentin Tolisso, while the visitors made only four changes to the side that started the 4-1 World Cup qualifying win over Israel last Friday.
Mbappe and Spain captain Andres Iniesta came closest to opening the scoring before Griezmann saw a header ruled out early in the second half after the referee consulted with the VAR, which was first used in an international match in France's 3-1 friendly win over Italy last September.
A clumsy challenge from Laurent Koscielny on Deulofeu allowed Silva to score his 30th international goal from the spot, before Deulofeu doubled the lead with his maiden Spain strike at the end of a superb passing move, with the VAR again used to good effect after the linesman initially raised the offside flag.
The defeat is France's first at home – excluding Euro 2016 – since a 4-3 loss to Belgium in June 2015, while Spain have now won six of their eight matches under head coach Julen Lopetegui.
8 - Sergio Busquets is the only player to have started in all the eight games for under Julen Lopetegui. Essential. pic.twitter.com/XCtKXXbmY1— OptaJose (@OptaJose) March 28, 2017
Mbappe needed just five minutes of his first start to test David de Gea in the Spain goal, his flicked effort from Layvin Kurzawa's cross kept out of the net by the foot of the Manchester United man.
Gerard Pique hooked a promising Koscielny header away, but Didier Deschamps' men were being forced increasingly deeper as Spain began to assume control of possession.
Lopetegui's side were looking the more likely to break the deadlock. Iniesta brought a good low save out of Hugo Lloris at his near post after a fine pass from Pedro, before Isco shot into the arms of the France skipper from 20 yards out.
Griezmann thought he had snatched the lead for the home side just after half-time, heading beyond De Gea after Kurzawa nodded down Christophe Jallet's delivery, but the goal was disallowed for offside after the referee consulted with the video assistant.
Felix Zwayer referred the decision – even as France players celebrated with Griezmann – before awarding Spain a free-kick and the footage confirmed that both the Atletico Madrid forward and Kurzawa had strayed beyond the last defender when Jallet crossed the ball.
Mbappe sliced a half-chance wide after working space inside the area, but Spain were gifted the breakthrough in the 68th minute by a clumsy piece of play from the hosts.
Tiemoue Bakayoko's pass was cut out by substitute Deulofeu and when Koscielny clumsily bundled the AC Milan loanee to the ground, Silva stepped up to sweep the penalty kick confidently into the bottom-right corner.
9 - David Silva has been involved in more goals for than any other player under Julen Lopetegui (six goals and three assists). Magic. pic.twitter.com/qzqHFCFlLs— OptaJose (@OptaJose) March 28, 2017
France pushed for a leveller, but a stylish counter-attack from Spain put the result beyond them. Sublime skill from Sergio Busquets allowed Silva and Jordi Alba to combine down the left and the Barcelona full-back's low cross was tapped into the net by Deulofeu, who had escaped Samuel Umtiti.
The linesman ruled that Deulofeu had scored from an offside position, but the VAR once more ensured the correct call was made, as the video showed the winger had just managed to remain level before converting from eight yards out.