Gyasi Zardes made it three wins from three matches since Berhalter's appointment after breaking the deadlock nine minutes from time in Orlando.
Zardes' long-range shot deflected off a defender and looped over Ecuador goalkeeper Alexander Dominguez as Berhalter became just the second USA coach after Bob Bradley in 2007 to win each of his first three games.
USA was flawless heading into the international fixture after wins against Panama and Costa Rica and it made a bright start.
Paul Arriola, Christian Pulisic and Zardes were in the thick of the action against Ecuador, who had a lot to thank Dominguez for during the early exchanges.
Ecuador – headlined by Manchester United veteran Antonio Valencia earning his 94th cap – slowly found its feet and started to get on the ball, though the USA should have taken the lead approaching the half-hour mark.
Some lovely interchange play between Zardes and Pulisic set up Arriola with a one-on-one chance just outside the six-yard box but Dominguez used his outstretched leg to thwart the Americans.
Berhalter's men did put the ball in the net four minutes later, however, it was ruled out of for offside, though replays showed it was a very close call on Jordan Morris.
Ecuador – which failed to qualify for the 2018 World Cup like United States – managed to get in behind before half-time thanks to Beder Caicedo, whose shot flashed just over the crossbar in a timely warning for the hosts.
The South American visitor defended well and continued to do so in the second half amid a host of substitutions for both sides, which impacted the rhythm of the match.
Ecuador – which offered little in attack – looked comfortable in defence as they match appeared to be petering out for a draw.
However, Dominguez went from hero to villain after he was caught scrambling off his line by Zardes, who secured a third successive victory and clean sheet.