Khoukhi powered home Homam Ahmed's cross in the 94th minute to cancel out Breel Embolo's first-half penalty and snatch a point that left all four teams in Group B level after one round of matches.
For Lopetegui, however, the significance of the result stretched beyond the standings.
"We achieved one dream when we arrived here, to be here, and now today is another little dream," the Spaniard told reporters.
"And we have the right to continue having the dream."
The late goal sparked jubilant celebrations among Qatar's players after they spent much of the match absorbing Swiss pressure, with Switzerland registering 26 attempts on goal to Qatar's seven.
Lopetegui said his side never abandoned the game plan, even after falling behind in the 17th minute.
"We made very few changes, but we had to keep our plan because if you... want to open too early against a team like Switzerland, you will suffer a lot," he said.
Qatar remained compact and disciplined, continuing to defend in numbers rather than chasing the game, a strategy Lopetegui said was necessary against a side boasting top-level talent throughout the squad.
"We believe, we work, we resist, we are resilient," he said. "In the end, we have one big award for us."
Lopetegui reserved special praise for his players' mentality, saying he would have been proud of their effort even without Khoukhi's dramatic equaliser.
"I was very proud about the mentality, about the discipline that they showed today," he said.
Lopetegui quickly turned his attention to Thursday's meeting with co-hosts Canada, warning that recovery would be crucial after a physically draining contest.
Qatar have one day fewer to recover than Canada and must travel before the match, while many of Lopetegui's players are still adapting to the demands of World Cup football.
"Our players need sometimes more time than the rest of the players because they are not used to this kind of rhythm," he said.
"We have to make one big effort to recover well and to be ready for the next big, big challenge."
For now, though, Qatar's campaign remains alive.
"It's going to be tough, difficult," Lopetegui said. "But we win our right."