Le Roy lost his first competitive game in charge of DR Congo
Uganda ensured DR Congo's miserable year continued as the Cranes won 1-0 in Kampala on Sunday.
Ibrahim Sekajja scored the winning goal after 76 minutes to settle the Group Two qualifier.
The Cranes started the match brightly, and Hassan Muviru hit the post after just eight minutes with the visiting goalkeeper beaten.
Uganda continued to dictate, with captain David Obua going close midway through the first half.
Milambo Mkamba had an opportunity to put the Simbas in front shortly before half-time, but he blazed wildly over the bar when well-placed.
In the opening stages of the second half, Kaluyitu Kalioku missed another glorious chance for DR Congo as he shot wide after cutting in from the right-hand flank.
The home side then exerted considerable pressure on the Simbas, with Muviru missing a sitter after 51 minutes and then a dangerous free-kick from Uganda captain David Obua was almost touched home just five minutes later.
With fourteen minutes left, Sekajja found the back of the net following a Ugandan corner and the lead looked in danger when DR Congo's Kabamba Muahah almost steered his header home in stoppage time.
Lomana LuaLua missed the match, which was an inauspicious start for DR Congo's new French coach Claude Le Roy, as the striker served one game of a four-match suspension following his sending-off in the 2004 Cup of Nations.
The Simbas lost all their group games in Tunisia.
On Saturday, South Africa defeated a spirited Cape Verde side 2-1 in Bloemfontein to assume early pole position in Group Two of 2006 World Cup qualifying.
Cape Verde's Pedro Brito Butista rises above South Africa's Siyabonga Nomvete
Bafana Bafana opened their group campaign with victory thanks to a match-winning performance from captain Mbulelo Mabizela, who scored both goals.
Yet the 2010 World Cup hosts were handed a massive scare by the islanders and were fortunate to win, especially after falling apart when Cape Verde scored late on.
"At 2-0 up, we were coasting but then we panicked after they got a goal back and we needed much more discipline," said new Bafana Bafana coach Stuart Baxter.
Just before half-time, Mabizela blasted home a free kick which the Cape Verdians had given away on the edge of their area.
The wall jumped over the ball to make the South African's job easier but the goal came as much relief after a team ranked 144th in the world had proven surprisingly dangerous against a tacky South African defence.
The goal was Mabizela's first at international level, and he did not have to wait long for his second.
The 23-year-old seemingly put the result beyond doubt when he blasted a stunning shot from nearly 40 yards out in the 70th minute to double Bafana Bafana's lead.
But eight minutes later, the Cape Verdians pulled a goal back through Janicio, whose shot was brilliantly volleyed home from the edge of the area after a pass laid back into his path by Carlos 'Calo' Morais.
Then Calo rounded South African goalkeeper Hans Vonk only to hit his goal attempt into the side netting, and then Lito missed another brilliant opportunity to equalize for Cape Verde right at the death.
South Africa's next Group One fixture is in a fortnight in Kumasi, where Ghana are likely to prove Bafana Bafana's toughest opponents for a place in Germany.
However, the Black Stars went down 1-0 to Burkina Faso in Ouagadougou.
Vitesse Arnhem striker Mamadou Zongo finally broke the deadlock in the 80th minute, when the substitute headed home from a free-kick from Florent Rouamba.
Juventus midfielder Stephen Appiah was thus left to curse his first-half strike which thumped against the Burkinabe crossbar after 13 minutes.
After the match, Ghana defender Samuel Osei Kuffour, who plays for Germany's Bayern Munich, was taken to hospital for examination of a shoulder injury suffered near the end of the tie.
The 2006 World Cup qualifiers double as qualifying matches for that year's Cup of Nations in Egypt.