How to format a java.sql.Timestamp(yyyy-MM-dd HH:mm:ss.S) to a date(yyyy-MM-dd HH:mm:ss)

You do not need to use substring at all since your format doesn't hold that info.

SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
String fechaStr = "2013-10-10 10:49:29.10000";  
Date fechaNueva = format.parse(fechaStr);

System.out.println(format.format(fechaNueva)); // Prints 2013-10-10 10:49:29

A date-time object is not a String

The java.sql.Timestamp class has no format. Its toString method generates a String with a format.

Do not conflate a date-time object with a String that may represent its value. A date-time object can parse strings and generate strings but is not itself a string.

java.time

First convert from the troubled old legacy date-time classes to java.time classes. Use the new methods added to the old classes.

Instant instant = mySqlDate.toInstant() ;

Lose the fraction of a second you don't want.

instant = instant.truncatedTo( ChronoUnit.Seconds );

Assign the time zone to adjust from UTC used by Instant.

ZoneId z = ZoneId.of( "America/Montreal" ) ;
ZonedDateTime zdt = instant.atZone( z );

Generate a String close to your desired output. Replace its T in the middle with a SPACE.

DateTimeFormatter f = DateTimeFormatter.ISO_LOCAL_DATE_TIME ;
String output = zdt.format( f ).replace( "T" , " " );