He opened fire on the Ozar Hatorah school in the north-east of the city, also seriously injuring a teenage boy.
The attacker fled on a scooter, in similar style to the killer of three soldiers in two separate incidents in the same part of France last week.
Police say the same .45 calibre gun was used in all three attacks. The search for the killer is now under way.
A special service in memory of the victims will be held at one of the synagogues in Toulouse at 17:00 (16:00 GMT). There will also be a silent march in Paris at 20:00.
President Nicolas Sarkozy, who flew to Toulouse, described the attack as a “national tragedy”. He has called for all schools in France to observe a minute’s silence on Tuesday and vowed to hunt down the killer. Read more at the BBC….