1999 proved to be a watershed year. Yoong's sponsors dropped out, and his father was forced to fund his son's racing activities until the family became indebted. He missed the first two rounds of the year but made a strong comeback when he returned at Thruxton. Driving a Dallara F399 Mugen Honda, Yoong finished sixth, 11 seconds behind winner Jenson Button. He followed this strong finish with 5th at Brands Hatch, in a race that covered the top seven by 3.4 seconds. The second race at Brands Hatch saw Yoong record a second-place behind Narain Karthikeyan, which was followed up with another sixth at Oulton Park before leaving the series for Formula 3000. This result confirmed, Yoong moved up from 268th to 214th in the world rankings. Overall, Yoong finished 11th in the championship.
During the off-season, Yoong tested for both the Nakajima and Le Mans Formula Nippon teams. His first trial at Suzuka took place on 8–9 December 1999 attended by ex-Formula One driver Satoru Nakajima after Yoong set a lap that made him fifth fastest out of 12. Nakajima said of Yoong "Alex is very much better than I originally thought". Yoong spent time at the Bukit Jalil institute with psychologist Michel Gagne and trainer Jorg Teichmann to recuperate from his injuries at Spa the previous year. His Formula Nippon career started disastrously at Suzuka after crashing his Reynard 99L Mugen at 250 km/h at the daunting 130R in qualifying and forced Yoong to miss the race. At Motegi, a mechanical failure stalled his car at the start at Mine after starting seventh, where he went on to cause a multi-car pile-up in desperation to climb back up the field. Yoong's team manager, K. Homma told him he needs to calm down and finish races, and his father Hanifah encouraged him to take off the pressure.