If you have shorted out the PSU at the incoming power plug of the video card, then hopefully, there is no damage to the video card (as you probably weren't drawing the short through the video card and motherboard)

Are you positive that you didn't have the probes connected to the current measuring plugs on your multimeter. This would definitely short out between the red and black cables.

The PSU would have shut off due to overcurrent limits, which causes a polyfuse to disable the PSU. Once the polyfuse cools down (10 minutes or so), it resets and you can use the PSU. Saves a lot of RMA and customer support frustration over blowing a normal fuse!

Basically I have never measured current with that multimeter, So the lead has never been connected to that current measuring connector.

I did put black lead to second to bottom pin first and then I touched the bottom pin with red lead and I got the spark. Difficult to understand what happened. Only thing that would make sense would have been if the red lead touched accidentally the both 2 bottom pins at same time but I thought I was being careful.

Well, the card is probably broken because it thinks that the power cable isn't connected even when it is and I have tried it with 2 motherboards too, but it is good that the psu didn't fry there. I would not have had a replacement psu for that system.

If you touched the metal of the heatplate with the red lead while in contact with the bottom pin, that would also short PSU, as the heatsink is often attached to ground.