The Monegasque retired from the season-opening race in Bahrain on March 5th with a loss of power, a failure blamed on the control electronics that had already been replaced on Sunday morning.
Drivers are allowed two control units to last the entire season.
"Unfortunately, it was two times the control electronics box and it's something that we never experienced in the past," Vasseur told reporters ahead of Sunday's second race of the season.
"I hope that now we have it under control. We have a deep analysis on this. Unfortunately, we'll have to take the penalty in Jeddah because we only have a pool of two control electronics for the season."
Leclerc finished second with the fastest lap to Red Bull's world champion Max Verstappen (25) in Jeddah last year, with Spanish teammate Carlos Sainz (28) third at a track that could favour Ferrari's straight-line speed.
Verstappen won the season-opener in Bahrain in a Red Bull one-two with Mexican Sergio Perez (33) and they are favourites to win again on Sunday in Saudi Arabia.
Engine reliability was a problem for overall runners-up Ferrari last year, as well as strategic errors and driver mistakes.
Vasseur has taken over from departed principal Mattia Binotto with the Italian team already on the back foot as they chase a first title since 2009.
The Frenchman also confirmed that senior engineer and aerodynamics expert David Sanchez had left the team after a decade at Maranello, but played down reports of more high-profile departures.
"We are a solid group and we are building up a team for the future also, and the link is good. So no, I don't think that key people will leave the team," he said.
