The Madrid event is due to take place on April 28th and Jimenez said that it would go ahead with greater security measures in place after Monday's twin bomb blasts that killed three and injured more than 100 in Boston.
"We have met with those responsible for the infrastructure at local government and we will speak with a government delegation," Jimenez told reporters on Tuesday.
"We continue as planned, with sadness, but the Madrid marathon will go ahead. We will take the necessary measures.
"We are going to perform some type of tribute to the victims and organisers of the event in Boston. We still don't know in what exact form, but we will do it."
The president of Madrid's bid for the 2020 Olympic Games, Alejandro Blanco, meanwhile expressed his dismay at the targeting of such a popular and historic sporting event.
"A marathon, and especially a people's marathon, is a celebration of sport," he said in an emailed statement.
"It is the best possible demonstration of how thousands of people can push themselves to new limits to finish the race, driven by nothing more than their own effort, enthusiasm and courage.
"All of us at the Madrid 2020 Bid would like to express our sincere and total support for the athletes, their families, the organisers, the US Olympic Committee and all the people of the USA, who have suffered as a result of this barbaric act. We are right by their side."
The Spanish capital is up against Tokyo and Istanbul in the bid to host the Games in seven years' time.
The head of the Tokyo bid, Tsunekazu Takeda, and Professor Ugur Erdener, president of the Turkish national Olympic committee, also expressed their condolences.
Takeda described the attack as a "senseless act" while Erdener described it as "a truly sad day for world sport".
"However, like the spirit of the marathon runners, sport will rise above these acts of evil and continue to be a force for good the world over," Erdener added.