Spain and France have met 34 times so far and Spain have had more success with 15 victories, while France celebrated in twelve of those games.
And so the goal was disallowed and Spain eventually won 2-0.
"For sure the result would not have been the same", Deschamps said.
"It's perfectly understandable that the coach has concerns about our game time here, but for me, nothing is more important than the France team", he declared before touching on the fact that there are also five PSG players in the France squad.
With the French League Cup final between Paris Saint-Germain and Monaco scheduled on Saturday, Deschamps rotated his team.
After thrashing Israel 4-1 at the weekend - with goals from David Silva, Vitolo, Diego Costa, and Isco, Spain head into the France game in good spirits, hoping that they can win their second game in the space of three days.
Before kick-off, respects were paid to former France and Real Madrid midfielder Raymond Kopa, who died earlier this month.
German referee Felix Zwayer made full use of the Video Assistant Referee (VAR) system being trialled by Federation Internationale de Football Association as an opening goal for the hosts was disallowed for offside, while an incorrect flag against Gerard Deulofeu for Spain's second strike was overturned.
Iniesta got his team's first chance when he curled a shot just wide from inside the box in the 14th minute. Technology was involved again in the 77th minute to overturn an incorrect offside call against Deulofeu after his close-range finish to make it 2-0.
Spain thought they had taken the lead in the 23rd minute when Pique knocked the ball in from a corner, but the referee ruled there had been a foul by Sergio Ramos on France goalkeeper Hugo Lloris.
Federation Internationale de Football Association announced the trial previous year, allowing the head referee to ask for a review of game-changing moments: plays with goals scored, penalties and even red cards.
"Deulofeu was decisive, if he keeps playing like this, he's got a bright future in front of him", Lopetegui said.
It's not been all doom and gloom for Spain, though, as La Roja are unbeaten in World Cup qualifying since 1993 and lead their current qualifying group for Russian Federation 2018 on goal difference above Italy.
Spain, who top Group G, visit Macedonia on June 11.