Magnussen managed a best time of1:29.517s, just 0.06s down on his team-mate.
It was an effort that was just a tenth shy of that which would have seen him through into Qualifying 3.
“The car had good potential to be in the top 10,” Magnussen said.
“It was very tight, so with these issues you very quickly lose some performance.
“With the brake issue I had and then also in qualifying the downshifting issue, it's a big penalty when it's this tight in the midfield, or the whole field.”
Magnussen was uncertain whether the two issues were related.
The brake issue reared its head in Free Practice 2 and persisted through Free Practice 3.
The downshifting issue then appeared in qualifying.
“They're not gripping enough, and inconsistent corner by corner,” he explained of the brake problem.
“So it makes it tricky.
“I don't think it's anything that we're doing to it. I don't know what it is.”
Magnussen pleased with progress despite issues
Issues aside, Magnussen believes Haas has made progress as the weekend in Jeddah has worn on.
“We were much more on the pace today,” he reasoned.
“Being this close to the front with all these issues that we had, that was kind of surprising.
“So I think we made some good progress and got to be happy with that,
“Hopefully tomorrow we can manage the race well, not have too much tyre degradation like we had in Bahrain.
“I think we have a better understanding of what the car wants to do naturally and what the tendencies are with this car and just made some different set-up directions and the one we are at now feels like a good one,” he added.
“It shows, I think. We were competitive in qualifying despite the issues we had, and hopefully in the race tomorrow it will also be the case.”
Sunday's Saudi Arabian Grand Prix begins at 18:00 local time (04:00 AEDT Monday).